1. Installing and Loading Packages

This first block of code installs and loads all the libraries needed for the analysis. The include=FALSE option in the block header ensures that the installation commands and loading messages will not appear in the final HTML report, making it cleaner.

2. Data Loading and Preparation

Here, we load the raw count table and gene annotations directly from the GEO repository.

# Load GEO score table
urld <- "https://www.ncbi.nlm.nih.gov/geo/download/?format=file&type=rnaseq_counts"
path <- paste(urld, "acc=GSE186063", "file=GSE186063_raw_counts_GRCh38.p13_NCBI.tsv.gz", sep="&");
gset<- as.matrix(data.table::fread(path, header=T, colClasses="integer"), rownames="GeneID")

# Load gene annotations
apath <- paste(urld, "type=rnaseq_counts", "file=Human.GRCh38.p13.annot.tsv.gz", sep="&")
annot <- data.table::fread(apath, header=T, quote="", stringsAsFactors=F, data.table=F)

# Load the dataset
gse <- getGEO("GSE186063", GSEMatrix = TRUE, AnnotGPL = TRUE)
## Found 1 file(s)
## GSE186063_series_matrix.txt.gz
## Annotation GPL not available, so will use submitter GPL instead
gse <- gse[[1]]

# Extract phenotype data
pheno_data <- pData(gse)
pheno_data <- pheno_data[, c("title", "geo_accession", "diagnosis:ch1", "source_name_ch1")]

3. Selection of 433 genes

Gene selection performed by text mining and functional enrichment.

#Define genes of interest
genes_of_interest <- c(
  "ABCB11", "ABCD2", "ACE", "ACKR2", "ACP5", "ACP7", "ADAMTS9", "ADCY7", "ADGRL2", "ADIPOQ", "AHR", "AIM2", "AKAP13", "ALB", "ANKRD55", "ANXA1",
  "APOL1", "APOL6", "AQP1", "AREG", "ARHGEF3", "ATG16L1", "ATG5", "ATOX1", "ATXN2L", "BEND2", "BGLAP", "BMP2", "BMP7", "BNIP3L", "BRAF", "BTG1",
  "C15ORF48", "C7ORF57", "CALD1", "CAPS2", "CARD9", "CASP1", "CASP10", "CAST", "CCL2", "CCL20", "CCL25", "CCL3", "CCL5", "CCND1", "CCND3", "CCR2",
  "CCR6", "CCR7", "CCRL2", "CD14", "CD160", "CD19", "CD274", "CD28", "CD36", "CD38", "CD3E", "CD4", "CD40", "CD40LG", "CD52", "CD63", "CD68",
  "CD69", "CD80", "CD83", "CD86", "CD8A", "CD8B", "CDC42BPB", "CEBPA", "CEBPG", "CENPK", "CLEC2B", "CLEC4D", "CLIC3", "CMAHP", "CMTM2",
  "COL1A1", "COX2", "CRB1", "CREM", "CRP", "CSF2", "CSMD1", "CSN3", "CSNK1A1", "CTLA4", "CTSB", "CTSK", "CUX1", "CX3CR1", "CXCL10", "CXCL13",
  "CXCL16", "CXCL2", "CXCL8", "CXCR2", "CYCS", "CYP1A1", "CYP4F22", "DDIT3", "DDX60", "DKK1", "DLAT", "DNAJA2", "DNAJB6", "DUSP4", "DYSF",
  "EDNRA", "EFCAB13", "EFCAB7", "EGF", "EGFR", "EGR3", "EIF5B", "ENO1", "EOMES", "ERAP1", "ERAP2", "ERN1", "ERP44", "EZH2", "FAXDC2", "FCGR1A",
  "FCGR2A", "FCGR3A", "FGB", "FNBP1", "FOS", "FOSL1", "FOSL2", "FOXP3", "FRZB", "FUT2", "GAPDH", "GATA3", "GBP1", "GBP3", "GBP5", "GEM", "GINS1",
  "GJB2", "GJB6", "GLUL", "GOLIM4", "GPR35", "GPT", "GZMA", "GZMB", "GZMK", "HCAR3", "HERC6", "HHAT", "HIF1A", "HK2", "HLA-A", "HLA-B", "HLA-C",
  "HLA-DQB1", "HLA-DRB1", "HSPA5", "HSPA6", "HYAL4", "ICAM1", "ICOS", "IFI16", "IFI6", "IFIH1", "IFIT3", "IFNA1", "IFNG", "IFNGR1", "IFNLR1",
  "IGF2", "IGF2-AS", "IL10", "IL12B", "IL13", "IL15", "IL17A", "IL17F", "IL17RA", "IL18", "IL1A", "IL1B", "IL1F10", "IL1R1", "IL1RN", "IL2",
  "IL21", "IL21-AS1", "IL22", "IL23A", "IL23R", "IL2RA", "IL33", "IL36RN", "IL37", "IL4", "IL5", "IL6", "IL6R", "IL7", "INS", "INS-IGF2", "IRAK1",
  "IRS1", "ITGA2B", "ITGAL", "ITGAM", "ITGAX", "JAK2", "JAK3", "JDP2", "JRKL", "JUN", "JUNB", "JUND", "KANK4", "KDM5B", "KIR2DS1", "KIR3DL1",
  "KIR3DL2", "KLRB1", "LAMP1", "LAMP2", "LEP", "LILRA5", "LILRB2", "LINC01185", "LINC01250", "LMO7", "LPAL2", "LRRK2", "LTA", "LURAP1L",
  "LURAP1L-AS1", "LYZ", "MAF", "MBL2", "MCAM", "MCL1", "MEFV", "MICA", "MIR146A", "MIR21", "MIX23", "MMP1", "MMP3", "MMP7", "MMP9", "MRPS23",
  "MSN", "MTHFR", "MUCL1", "MX1", "MYC", "MYNN", "NABP1", "NAMPT", "NCOA7", "NDUFS1", "NFKB1", "NKG7", "NLRP3", "NMI", "NOD2", "NOS2",
  "NOXRED1", "NPEPPS", "NRG1", "NT5C3A", "OLR1", "OSMR", "PDCD1", "PDLIM7", "PER1", "PFDN4", "PFDN5", "PFKL", "PGD", "PGK1", "PHEX", "PI3",
  "PIK3CD", "PINK1", "PLA2G4D", "PLCG1", "PLG", "PLIN5", "PLS1", "PPARD", "PPARG", "PPARGC1A", "PPARGC1B", "PRDM1", "PRF1", "PRTN3", "PSG2",
  "PSMC2", "PSMD7", "PSME2", "PTGS1", "PTGS2", "PTH", "PTPN22", "PTX3", "PYGL", "RAC1", "RBM45", "REL", "RETN", "RGPD6", "RIT1", "RORC", "RPL15",
  "RPL36AL", "RPL41", "RPL7", "RPS19", "RPS21", "RPS26", "RPS6KB1", "RPS7", "RSAD2", "RUNX2", "RUNX3", "S100A12", "S100A8", "S100A9", "S100P",
  "SAA1", "SAMD9", "SAR1A", "SCN1A", "SEC14L2", "SEC24B", "SELL", "SERPINA1", "SERPINB1", "SERPINE1", "SF3B1", "SF3B3", "SGK1", "SH3BGRL3",
  "SIAH1", "SLC1A2", "SLC2A3", "SLC51B", "SLC7A11", "SLC7A5", "SMAD3", "SMARCA4", "SMOX", "SOCS1", "SOD2", "SOST", "SOX4", "SP7", "SPCS3",
  "SPON2", "SPP1", "SSR1", "STAT1", "STAT3", "STIM1", "SUOX", "SYT1", "TALDO1", "TBX21", "TEK", "TFPI", "TGFA", "TGFB1", "TGFBR3", "TIMP1",
  "TLR2", "TLR3", "TLR4", "TLR9", "TMBIM6", "TMEM45A", "TMPRSS11B", "TNF", "TNFAIP3", "TNFAIP6", "TNFAIP8", "TNFRSF10A", "TNFRSF1A",
  "TNFRSF1B", "TNFRSF9", "TNFSF10", "TNFSF11", "TNFSF13B", "TNFSF15", "TNIP1", "TOMM5", "TOMM7", "TPST2", "TPT1", "TRAF2", "TRAF3IP2", "TRAF4",
  "TRAF5", "TRBV20OR9-2", "TRIM22", "TRIM69", "TTC39B", "TYK2", "TYMP", "UBE2L3", "UQCR10", "UTP11", "VCAM1", "VDR", "VEGFA", "VIM", "WDR1",
  "WNK1", "WWOX", "XAF1", "XBP1", "YOD1", "YWHAB", "ZC3H12A", "ZFP36", "ZMIZ1", "ZNF316", "ZNF415", "ZNF483"
)

# Load the data.table package
library(data.table)

# Keep only the notes for the genes of interest.
 annot_filtered <- annot[annot$Symbol %in% genes_of_interest, ]
 
 # Filter the count matrix using GeneIDs as the key (MUCH MORE SECURE)
expr_data_filtered <- gset[rownames(gset) %in% annot_filtered$GeneID, ]
 
# Filter expression data for genes of interest
express <- rownames(expr_data_filtered)

# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(expr_data_filtered), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Replace rownames with gene symbols
rownames(expr_data_filtered) <- gene_symbols

# View the updated dataframe
print("Data frame com rownames modificados para símbolos de genes:")
## [1] "Data frame com rownames modificados para símbolos de genes:"
print(expr_data_filtered)
##             GSM5629971 GSM5629972 GSM5629973 GSM5629974 GSM5629975 GSM5629976
## TNFRSF9             50          3         13         28        226         12
## ENO1             21517       9106      21132      18757      21238      19317
## PIK3CD             491        284        584        344        412        393
## PGD               3456       2524       2100       1472       1664       2020
## MTHFR             1060        507        939        665        731        654
## TNFRSF1B          1522        477       1075        644       1401        884
## PINK1             1388       1164       2344       1475       1376       2275
## IFNLR1             194        222        508        333        225        371
## RUNX3             1255        745       1978       2018        903       1513
## SH3BGRL3          4651       1901       3289       1491       5552       3202
## CD52               833        282        290        109        972        219
## IFI6              5034        369        995       1873       8368        937
## ZC3H12A           3980        386        547        460       1318        549
## UTP11             1222        584        951        528       1194        764
## JUN               1725        886       2180       1888       3261       2115
## KANK4               43         74         84        135          5        127
## EFCAB7             116        148        255        182        168        199
## IL23R               15          3          2          1          0          3
## ADGRL2             957        468        747        687        589        749
## GBP3              1429        381        692        337       1082        390
## GBP1              2993        441        573        464       8242        717
## GBP5               535         71        135         99       1030        179
## TGFBR3            1977       1607       3344       2129        860       2725
## VCAM1              593        170        324        142        959        330
## PTPN22             146         39         50         37        218         53
## CD160               18         13         19         21         15         20
## FCGR1A              88          9         11          7        117          9
## MCL1              6253       2815       5078       4115       9390       5234
## CTSK              9277       2985       8517       4164      16149      16807
## RORC               191        516       1280        694        143        726
## S100A9          348987        955        265        258     100573        267
## S100A12           1383          4          8          1         45          2
## S100A8          332188       2023        151        703      94403        316
## IL6R               642        350        764        496        895        610
## RIT1               712        269        605        464        784        559
## BGLAP               19         12         49         32         22         25
## IFI16             6282       2358       3302       2500       5130       2969
## AIM2                81          7         15          7        197         29
## CRP                  0          0          0          0          0          1
## FCGR2A             305         75        141        109        579        234
## HSPA6              327        112        141        105        345        138
## FCGR3A             393         19         72         12        638         51
## SELL               232         29         84         28        319         89
## GLUL             15899       5989      11400       8059      10581      10486
## PTGS2               58         16         21         30        141         53
## CRB1                 0          3          8          7          2         19
## KDM5B             1834       1348       2331       1351       1237       1691
## IL10                10          4          2          6         23         10
## YOD1              1154        341        558        220       1086        420
## HHAT               171        180        226        145        142        226
## TRAF5              299        176        422        283        405        454
## NLRP3               82         24         33         26         89         63
## LINC01250            0          1          0          0          3          2
## RPS7             40511      21792      33674      13292      28269      19242
## RSAD2              420         75        144        133        857        139
## FOSL2             5364       2081       4251       3443       3101       4891
## REL               2081       1014       1504       1072       1230       1106
## TGFA              1015        261        581        382        798        389
## DYSF               721        152        352        321        313        509
## HK2               2276        562        793        664       1335        750
## CD8A               503        139         89         62        533         63
## CD8B               230         72         79         32        204         35
## EIF5B             6100       6040      10250       3943       3310       4873
## IL1R1             2777       1279       2702       1680       1706       2279
## RGPD6              319        374        745        523        366        570
## IL1A                17          3         25         11         31         20
## IL1B                80         15          7          6         81          7
## IL37                97        159        765         34         89        297
## IL36RN            7721        213       1169         45       2673        547
## IL1F10              44         13         40          0         33         44
## IL1RN             1743       1081       2271        909       2206       1295
## NMI               1513        406        671        364       2232        540
## TNFAIP6             78         43         41         66        278        177
## IFIH1             1083        359        549        476       1291        397
## SCN1A                7         12          1          5         18         21
## ABCB11              29         71         45         18          4         26
## RBM45              182        150        202        144        161        201
## FRZB               543        476       2404       1361        714       2110
## TFPI               634        292        771        307        575        704
## STAT1             9452       1246       1844       1717      14555       2363
## NABP1              364        146        213        151        601        252
## SF3B1             5807       4764       8360       6821       5949       7962
## CASP10             569        209        458        311        528        426
## CD28               198         39         38         30        301         65
## CTLA4               67         13         22         29        350         27
## ICOS                71          3          9          8        267          9
## NDUFS1            2390       1623       2785       1952       1939       2320
## CXCR2              532        110        204         78         80        138
## IRS1               634        238        502        465        239        784
## CCL20               79          7          2         30         36          9
## ATG16L1            606        334        876        622        762        770
## GPR35               43         16         65         71         36         56
## PDCD1               55          7          8         12         97          8
## PPARG              182        549        318        245        129        378
## RPL15            40705      24784      49015      23424      33900      33086
## EOMES               34         18         27         11         57         22
## CX3CR1             209         56        106        109        148        118
## ACKR2              169         10         16         20         72         65
## CCR2               340        108        113        118        358        178
## CCRL2               51         13         34         18         48         26
## TLR9                27          4         11         13         22         23
## ARHGEF3           1188        576        788        745       1283       1059
## ADAMTS9            338        100        212        238        118        262
## TMEM45A          11615       4899       6159       1058       9951       4107
## CD80                18          2          3          4         50          7
## CD86               219         82        102         75        361        122
## MIX23              365        202        340        173        309        222
## PLS1               139         69        186        198         75        230
## PTX3                96         18         81         50         23         58
## GOLIM4            1334        544       1393       1287        872       2151
## MYNN               710        308        583        412        999        576
## TNFSF10           4857       1909       3406       2377       7441       2496
## ADIPOQ             632          5       1062       1316         19       1972
## SPON2             1090        332       1477       1218        841       1506
## S100P             2056        159       1625        921        313       1179
## WDR1              8397       2726       6846       5170       7197       6944
## CD38                54          9          7         12         53         28
## PPARGC1A           429        372       1180       1188        124       1059
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          1          0          0
## ALB                  2          3         10          5          1          8
## CXCL8              700          3          5          2        163          8
## CXCL2               88          5          1          3         75         13
## AREG               244         57        138        168        432         90
## CXCL10             707         32         11         13      13153         23
## CXCL13              97          2         12         12        374          9
## SPP1                85          5          3         12        111        434
## HERC6             1363        191        354        339       1848        329
## NFKB1             2457       1010       1957       1362       2084       1925
## SEC24B             957        687       1305        888        839       1201
## EGF                 61         17        140        168         12        109
## IL2                  1          3          0          0          5          0
## IL21                 0          0          0          0         25          0
## IL21-AS1             0          0          0          0          2          0
## SLC7A11            202         24         28          3         62         54
## IL15               163         63        127         78        287         92
## EDNRA              636        264        517        634        371        446
## TLR2               259        117        243        193        282        193
## FGB                  0          0          0          0          0          0
## DDX60             1919        313        675        436       2430        536
## SPCS3             2798       1306       1926       1266       2959       1876
## TLR3               209         75        137         98        224        170
## OSMR              1408        398        612        633        934        722
## GZMK               165         26         47         16        338         48
## GZMA               445         44         53         20        320         62
## ANKRD55             12         11          5          6         23         10
## CENPK              285         44         95        107        221         65
## CAST              8173       5028       9871       6765       6829       8803
## ERAP1             2395       1289       3103       1818       2842       2825
## ERAP2              256        191        314       1086        417        225
## TNFAIP8           1238        650        897        711       1821        931
## CSF2                 6          2          0          2         15          2
## IL5                  0          2         15          0          0          9
## IL13                 3          0          0          1         21          1
## IL4                  2          1          2          3          0          1
## CD14               734        207        449        317       1143        767
## CSNK1A1          12751       4632       8086       5212      11613       6640
## PPARGC1B           646        216        265        274        270        321
## TNIP1             3572       1317       3337       2164       3115       3120
## ATOX1              944        351        715        234        883        475
## FAXDC2            1100       1281       1897        986        442       1296
## IL12B                4          1          1          4         63          1
## MIR146A              4          0          4          1          2          1
## PDLIM7            1169        367       1517       1043        630       1062
## SERPINB1          3181        599       1454       1041       2754       1295
## SSR1              3066       1915       2842       1989       2784       2870
## CD83               475        136        196        216        773        216
## SOX4              1333       1248       2374       1978       1022       1780
## CMAHP              259        349        732        466        310        566
## HLA-A            27869      11994      30218      14566      50156      22146
## HLA-C            36794      13710      15819      10324      55997      23822
## HLA-B            40075      18918      40390      18616      70383      28987
## MICA               402        276        643        348        344        402
## LTA                 14         20         22         29         46         19
## TNF                 86         39         56         60        203         49
## HLA-DRB1          8538       3353       4656       5866      19692       7281
## HLA-DQB1           959        304        595       3905      10319       3414
## PPARD             2075        588       1207        785       1199       1013
## CCND3             1266        595       1494        963       1747       1349
## VEGFA             1237        671       1352       1109        986       1061
## RUNX2              138         61        156        186        124        196
## IL17A               20          0          0          4          0          0
## IL17F                8          0          0          0          1          0
## PRDM1             1485        285        334        188        911        264
## ATG5               998        478        744        615       1146        741
## TRAF3IP2          1364        644       1373        833       1111       1149
## NCOA7             1680        463        721        626       1985       1044
## SGK1              6110       1686       2741       3394       3440       4323
## IFNGR1            4381       1791       2704       1930       5251       2775
## TNFAIP3            997        465        468        418       1499        611
## SOD2             13755       2822       5586       4480      11205       5790
## LPAL2               12         10         28         10         29         20
## PLG                  2          2          3          2          0          0
## CCR6               145        101        108        125        181        120
## RAC1              8221       5163       9291       5149       7923       7016
## ZNF316            1094        724       1691       1341        551       1416
## AHR               3550       1824       3195       2178       3983       3017
## IL6                 26          2          4          1         30          3
## TOMM7             4508       3459       7723       3039       3313       3882
## CYCS              5730       1903       3287       2194       4958       3161
## AQP1              9494       4658      15763       8518       7003      12473
## NT5C3A            2163        538        605        350       1260        529
## EGFR              4740       3999       6609       6346       2130       7023
## CD36              4360       1444       2586       1371       2386       3441
## SAMD9              723        131        191        171        582        208
## SERPINE1           240         33         96        166       1099        129
## CUX1              1549        699       1865       1149       1075       1358
## PSMC2             3279       1581       2670       1579       3450       2426
## NAMPT             7998       1283       2396       1900       5149       2254
## HYAL4              214         25         82         55         56         23
## LEP                122          0        379        160          0        576
## CALD1             9548       3907      13284       6368       4055       8550
## BRAF               653        459        691        515        434        688
## EZH2               791        402        583        404        757        448
## DNAJB6            5337       2207       3733       2397       6204       2972
## CSMD1                3          8         29         23         16         54
## CTSB             12824       4960      11403       7090      15838      11175
## EGR3               791        572        478        200        613        362
## TNFRSF10A          298        158        170        142        479        193
## BNIP3L            3281       2711       3238       1767       3344       2515
## DUSP4              679        468        882        895        935        831
## NRG1               193        138        251        426        158        238
## RPL7             57360      53843      80676      38019      42107      52217
## IL7                150        104        205        119        251        155
## GEM                351        136        265        293       1272        274
## MYC               1962        621       1488       1059       1470       1187
## GPT                272        824        431        214         80        246
## JAK2              1065        449        625        445       1194        737
## CD274              231         39         37         39        333         57
## IL33              4734       1400       1895       1031       2980       2312
## LURAP1L-AS1          3          7          5          6          2         13
## LURAP1L            484        223        421        476       1246        537
## TTC39B            1448       1062        675        428       1235        661
## IFNA1                0          0          0          0          0          0
## TEK                615        198        619        384        208        519
## TRBV20OR9-2          0          1          0          0          0          2
## TOMM5             2010        667       1034        470       1307        774
## ANXA1             8480       5083      10080       7663      14230       9482
## ERP44             1481        848       1412        753       1346       1057
## ZNF483              91         96        320        178         69        219
## TNFSF15             66         26         46         64         37         77
## TLR4               457         99        275        133        533        563
## PTGS1             3895       2746       4917       1835       3037       3562
## HSPA5            11847       5770       7906       5068       7936       7342
## FNBP1             2326       1180       2144       1408       1881       1719
## CARD9              203         59        140        156        182        129
## TRAF2              418        339        733        418        610        486
## CLIC3             1341        247       1286        371        733        666
## IL2RA               70         25         21         43        356         56
## GATA3             1982       4126       8294       2604       1194       3715
## VIM              37725      16921      40825      19423      22308      36843
## CREM               479        182        402        248        571        350
## DKK1                27         24         95         55        120        177
## MBL2                 0          0          0          0          0          0
## SAR1A             2295       1449       2742       1813       2439       2543
## PRF1               230         32         62         36        241         70
## ZMIZ1             3075        963       2300       2203       1129       2924
## IFIT3             2321        400        739        623       4477        631
## TALDO1            4037       2856       3742       1744       3381       2316
## IGF2              1140        310        851        521        198        628
## INS-IGF2          1073        297        831        486        183        593
## IGF2-AS              1          2          6          0          0          0
## INS                  0          0          0          0          0          0
## STIM1             2133       1335       3168       2554       1844       3060
## TRIM22            2684        544       1184        824       4454       1386
## PTH                  0          0          0          0          0          0
## SAA1               558        166         89         40        297         71
## SLC1A2              33         49         60         77         52         79
## FOSL1              177          9         11         54        868         27
## CCND1             3724       4168       9545       5754       2075       6347
## JRKL               232        179        406        272        175        300
## MMP7               325        318       2227       1467        648       1323
## MMP1                84          3          8         88        441         14
## MMP3                26         14         39         42         74        125
## CASP1             2155        735       1097        619       2154        998
## DLAT              1057        491        681        714        900        986
## IL18              1999       2046       3503       1024       1775       2122
## CD3E               662        206        151        140        845        161
## MCAM              5876       1605       4526       2957       1595       3543
## WNK1              4629       2058       4058       3133       2561       5004
## TNFRSF1A          3743       1825       5012       2876       3570       3177
## GAPDH            37737      16153      50228      30954      31740      32595
## CD4               1385        435        661        559       1503        960
## SLC2A3             523        222        396        233        966        551
## CLEC4D               5          4          2          0         14          1
## KLRB1              162         49         50         19         94         40
## CD69               206         60         40         26        296         63
## CLEC2B            2881       2017       3357        982       2844       1708
## OLR1                14          2          4          4         10          8
## ABCD2               48         23         41         46         42         89
## LRRK2              471        168        449        276        536        553
## VDR               1348       1169       1148       1259        752       1287
## TMBIM6           13447      10875      14709      10999      11942      13219
## PFDN5             9570       5113       9743       4009       7347       5557
## SP7                  0          0          4          2          2          0
## MUCL1             7531       1489      19494       8928        849       8073
## CD63             12574       5589      15407       8681      14079      12806
## SUOX              1818       1436       2720       1646       1477       2022
## RPS26            13935       7524       4174       1936      11556       7536
## RPL41            89027      41784      79753      32959      66860      47160
## IL23A               29         10         24         28         20         14
## DDIT3              438        368        898        502        444        553
## IFNG                24          5          0          0         43          2
## IL22                33          0          0          0         16          0
## LYZ              12362       1130       1867       1435       9536       1960
## CAPS2               52         55        109        105         37         85
## SYT1                32         19         34         29          9         26
## BTG1              6465       5396       9564       4037       8597       7044
## HCAR3              574        281        349        114        793        192
## GJB2             23846       1593       4290       4236      10782       3088
## GJB6              5185       1217       2496       2690       3800       2191
## TNFSF11             19         11          3          1         32          2
## TPT1            169969      73868     117058      47799     126200      83602
## LMO7              1696        627       1549        990        993       1377
## TNFSF13B           435        121        165         80        621        174
## LAMP1             5967       3809       7624       4620       2806       6435
## PSME2             3130        998       1783       1156       4663       1256
## GZMB               438          7         19          6        347         20
## RPL36AL           5431       3762       6764       2829       5062       3459
## PYGL              2398        819       1822       1331       1555       1315
## HIF1A             3110        910       2077       3667       1935       2793
## FOS                683        474        904       1088       5229       1100
## JDP2               702        420       1287        719       1472       1207
## NOXRED1             34         19         44         35         18         33
## SERPINA1           291         38         74         70        443         95
## CDC42BPB          3315       1057       2753       2118       1549       3116
## PLA2G4D           3734        154        292         93        863        162
## TRIM69              36         15         50         27         57         20
## SLC51B              49         16         56         45         24         40
## SMAD3             1507        797       1622       1444        724       1714
## CYP1A1              62         26         69          1          0       1365
## AKAP13            2987       1586       3538       2779       1594       3378
## MEFV                44          5         15          8         18         13
## SOCS1              200         38        127        121        270        163
## ATXN2L            1706        829       1877       1659       1041       1668
## CD19                 3          5          7          9          3          3
## ITGAL              712        191        250        161        530        231
## ITGAM              335        117        170        112        327        320
## ITGAX              407        138        239        153        303        197
## DNAJA2            2998       1370       2762       1666       2979       2270
## SIAH1              685        676       1174        760        633        879
## ADCY7             1335        377        742        720        967       1179
## NOD2               749        207        352        211       1061        370
## CMTM2                1          7         12          7          5          9
## SF3B3             3670       1751       3302       2036       1894       2681
## PSMD7             3129       1923       2848       1659       3295       2423
## WWOX               308        181        255        209        213        223
## MAF               3593       3328       5732       3076       4168       4453
## SLC7A5            3753        653        935        553       1092       1231
## CXCL16            1456        485        647        638       1364        923
## XAF1              2060        738       1361       1142       2661        811
## CD68              1023        242        514        278       1409       1066
## PER1              2524       1940       5477       3879       2198       5712
## NOS2               161          4         24         23          5         20
## TRAF4              773        431       1221       1291        962        911
## CCL2               608        329        315        314        698        278
## CCL5               781        327        228        119        821        134
## CCL3                38          1          3          1         73         18
## CCR7               202         54         84         55        438         75
## STAT3            12150       4055       7443       6306       6117       7029
## SOST               472        172          0         29          4         37
## ITGA2B              12          7         30         25         11         15
## EFCAB13             49         84        195        111         32        123
## NPEPPS            2558       1240       2151       1636       2072       2276
## TBX21               35          9         20          8         35         11
## COL1A1           58802      15650      28578      40700      45110      56995
## MRPS23            1464        605        965        647       1293        898
## MIR21                0          0          1          2          0          2
## RPS6KB1            972        450        829        666        968        894
## ACE                882        197       1117        588        401       1084
## ERN1               619        262        665        574        384        632
## PRTN3                1          0          0          0          0          2
## PLIN5              532       1034        165         72         84        119
## RETN                 0          0          4          1          6          0
## CCL25                4          1          1          0          0          0
## ICAM1              706        281        608        329       1235        668
## TYK2              1484        727       1703       1595       1102       1750
## SMARCA4           3611       1863       4145       2980       1342       2589
## ACP5              1413        530        498        295       1633        543
## JUNB              4083       1307       3388       2177       7000       2491
## CYP4F22           1874        514        804         87        631        368
## JAK3               487        114        195        165        348        179
## JUND              2479       1554       3331       2235       4508       3261
## CEBPA             7062       3890       6238       2321       3870       4251
## CEBPG             2079       1334       2275       1429       2418       1894
## ACP7              1567         88        127         20        469         57
## ZFP36             1932        643       1280        914       2274       1291
## TGFB1             1768        528       1243       1001       1686        988
## RPS19            35572      22433      46604      17366      30996      26031
## PSG2                 0          1          1          0          0          2
## FUT2               374         71        325        155        188        181
## NKG7               221         21         51         20        204         51
## ZNF415             105         84        259        190        130        274
## LILRB2             265         38         72         51        178         95
## LILRA5              54          2          3          0         24          4
## KIR3DL1              0          0          2          0          0          0
## KIR3DL2             11          8          0          0          3          3
## SMOX               900         89        288        161        373        151
## BMP2               279        287        592        315        467        365
## GINS1              326        118        152        126        327        133
## PLCG1             2089       1124       2516       1909       1270       2110
## YWHAB            10093       7740      11220       5621       8925       8748
## PI3              31002         93        104          5       1682         75
## MMP9               260         50         44         96        764        287
## CD40               659        345        812        427       1077        507
## PFDN4              840        460        834        330        752        436
## BMP7               772        482        802        426        204        705
## RPS21            25233      10677      20028       7402      14336      10102
## MX1               3111        390        774       1088       2491        634
## PFKL              3770       1836       4874       3150       3237       4106
## IL17RA             927        500       1067        612        585        833
## UBE2L3            3000       1479       2648       1540       2675       2140
## TPST2             1006        426        979        535        959        857
## XBP1              5474       2163       4945       5453       3873       5117
## UQCR10            1801       1026       1437        756       1470       1059
## SEC14L2            373        172        400        430        314        409
## APOL6             3250        602        853        762       3301        894
## APOL1             1778        312        594        392       1600        491
## TYMP             10214        823       1029       1155      16254       1448
## BEND2                1          1          0          0          0          1
## PHEX                35          6         13         34         48         17
## TIMP1             1764        576       1751        930       1555       1659
## FOXP3              157         57         67         57        403         92
## MSN               9985       2642       5432       4385       8631       7037
## PGK1             11424       3784       7745       6380      13301       7879
## LAMP2             4464       3129       4978       4023       4737       4664
## CD40LG             107         68         22         21         60         25
## IRAK1             3129       1061       1801       1558       2539       2400
## COX2             55590      45347     119184      32088      11093      43778
##             GSM5629977 GSM5629978 GSM5629979 GSM5629980 GSM5629981 GSM5629982
## TNFRSF9             67         52          7         50          9         18
## ENO1             18134      32086      18427      23845      14243      18646
## PIK3CD             303        643        455        270        230        680
## PGD               4110       7442       1541       2889       5913       2652
## MTHFR              606       1180        831        735        591       1142
## TNFRSF1B           916       1270        751        804        597       1110
## PINK1             1662       4601       1914       1224       2573       2530
## IFNLR1             189        572        397        343        211        321
## RUNX3              943       1793       1365        378        528       1338
## SH3BGRL3          2773       4811       2450       5284       3531       3813
## CD52               422        421        227        573        278        508
## IFI6              1237        926        761      10302        518       1356
## ZC3H12A           1528       1909        724       5536       1172        712
## UTP11              687       1060        689       1724        663        849
## JUN               1532       2478       1221       1198       1469       2200
## KANK4               81        292         71          6        126        114
## EFCAB7             215        367        242        203        227        271
## IL23R                5          0          4          7          0          8
## ADGRL2             655       1621        710       1078       1167        973
## GBP3               613        899        595       1074        265        626
## GBP1               980        806        481       3755        570        589
## GBP5               242        209        106        727        107        240
## TGFBR3            1764       3767       2660        933       1819       3689
## VCAM1              391        537        261        507        402        598
## PTPN22             155        160         71        165         64        128
## CD160               17         39         20         19         22         30
## FCGR1A              23         18         11        175         22         23
## MCL1              3121       6672       4572       6921       4070       6050
## CTSK              5212      11733      14290      18078       9699      25688
## RORC               701       2363        564        131        760        895
## S100A9           21852       4827        189     655111       2408        638
## S100A12              9          0          1       4757          6         25
## S100A8           32680       6350        203     552503       2938        370
## IL6R               543        995        659        646        423        993
## RIT1               387        931        502       1046        458        893
## BGLAP               19         34         37         17         12         38
## IFI16             2578       3259       2438       4642       1550       3075
## AIM2                20         33         12        137         25         39
## CRP                  0          1          0          0          0          0
## FCGR2A             151        250        172        640        149        447
## HSPA6              110        182        159        386         96        222
## FCGR3A             117         70         39        627         79        145
## SELL                78         82         64        276         53        203
## GLUL             10003      17913       9185      26193       8478      16307
## PTGS2               26         71         24        352         18         49
## CRB1                 6         14          6          0          0          5
## KDM5B             1951       4134       1892       1320       1619       1876
## IL10                14          8          6         45          6         15
## YOD1               287        681        438       3475        606       1045
## HHAT               187        361        169        101        147        204
## TRAF5              295        594        494        264        279        762
## NLRP3               39         65         40        121         32         99
## LINC01250            0          2          0          0          1          0
## RPS7             26885      39359      20753      49551      25418      26466
## RSAD2              180        112        111       2313         84        187
## FOSL2             2209       6371       3344       3263       3694       3848
## REL               1029       1616        888       1416        897       1135
## TGFA               557       1339        357       3876       1056        782
## DYSF               146        422        308        325        342        494
## HK2                881       2510        603       2220       2236        843
## CD8A               193        226        125        181         86        190
## CD8B                69        104         74        136         69        129
## EIF5B             4482       6775       4322       2949       3617       4790
## IL1R1             1466       3153       2520       2065       1618       3108
## RGPD6              452        969        723        251        376        628
## IL1A                25         78         21        103         95         42
## IL1B                30         85          7       1039         61         21
## IL37                49        402        359        316        346        960
## IL36RN             163        564        514      27362        502       1301
## IL1F10               8         23         17        140         17         93
## IL1RN              845       2042       1573       4388       1095       1395
## NMI                683        735        557       2039        508        621
## TNFAIP6             57        107         92        457        143        150
## IFIH1              695        751        483       1386        347        668
## SCN1A                8         25          8          0         15         10
## ABCB11             104        254         34         19        139         27
## RBM45              153        299        227        222        153        228
## FRZB               610       2339       1859        288        321       1629
## TFPI               432        753        532        572        468       1165
## STAT1             2847       3380       1714       7997       1729       2423
## NABP1              305        539        287        867        275        526
## SF3B1             6203      12002       8625       6659       6219      11071
## CASP10             356        585        368        559        254        526
## CD28                91         95         46        135         40        126
## CTLA4               82         71         19         60         16         42
## ICOS                56         59         15         85         19         36
## NDUFS1            3112       6205       2450       2990       4185       3012
## CXCR2               91        140         64        495        121        162
## IRS1               386       1069        526        180        618       1439
## CCL20               24         11          8        101         10          5
## ATG16L1            632       1481        805        711        608       1192
## GPR35               41         97         63         25         20         73
## PDCD1               30         42         12         17         17         23
## PPARG              886       1404        208        182       1235        903
## RPL15            30127      57600      35584      53060      35342      48378
## EOMES               32         44         26         28         26         26
## CX3CR1             136        238        121        135        159        210
## ACKR2               20         56         25        354         56         54
## CCR2               239        387        176        340        234        410
## CCRL2               24         15         15        166         22         47
## TLR9                19         22         25         17         16         54
## ARHGEF3            554       1191        854       1172        622       1076
## ADAMTS9            128        294        243        120        164        239
## TMEM45A           8411      17313       2286      20537      15127       6663
## CD80                12          6          2         53          3          7
## CD86               159        218        136        436        115        244
## MIX23              285        352        227        451        220        279
## PLS1                84        200        208        172         75        182
## PTX3                26         68         44        205         58        196
## GOLIM4             627       1760       1627       1000        840       2445
## MYNN               493        942        600       1126        525        960
## TNFSF10           2760       3297       2390       6594       1570       3454
## ADIPOQ             146        153        715        314        585       5122
## SPON2              353       1112       1384        737        590       1760
## S100P              300        626       1152       3723        243        427
## WDR1              3766       9181       6192       7724       4868       6716
## CD38                 6          7         10         38          9         21
## PPARGC1A           495       1396        981        166        553       1049
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          4          0          0          0
## ALB                  6         13          4          0          9          2
## CXCL8               14          5          0      22721          8          3
## CXCL2               27         13          9        317          5         10
## AREG               103        128         76        434        172        112
## CXCL10             947        157          3        494        132         18
## CXCL13              59         37          1        161          4          7
## SPP1               136        106         30         79         11       1143
## HERC6              397        365        261       1560        167        314
## NFKB1             1158       2288       1568       1209        933       1699
## SEC24B             910       1715       1108        638        879       1264
## EGF                 82        317        119         11         65         90
## IL2                  4          1          2          1          0          0
## IL21                 6          2          0          5          0          0
## IL21-AS1             2          1          0          1          0          0
## SLC7A11             33         36         21        232         26         41
## IL15               104        157         96        178         91         99
## EDNRA              159        499        509        308        200        521
## TLR2               392        506        217        416        346        341
## FGB                  0          0          0          0          0          0
## DDX60              497        595        492       1879        352        886
## SPCS3             1810       3384       1816       3888       2044       2625
## TLR3               130        173        106        153        118        259
## OSMR               478        901        673       1069        607        937
## GZMK                64         93         22        160         69         54
## GZMA               119        140         25        335         98         68
## ANKRD55              3         14          6         11         14         23
## CENPK              143        163        159        417         89        103
## CAST              4867      10982       8420       8646       6743      11751
## ERAP1             1706       3601       2620       1789       2046       3366
## ERAP2              256        290       1048        178        161        317
## TNFAIP8            873       1281        969       1657        764       1287
## CSF2                 5         12          5         28          1         12
## IL5                  1          4          0          0          2          2
## IL13                 6         10          2          5          1          4
## IL4                  3          4          0          1          3          0
## CD14               504        968        455       2008        696       1738
## CSNK1A1           5016       9795       6580      13348       5522       7571
## PPARGC1B           518        835        340        370        457        401
## TNIP1             1901       4327       2448       4322       2239       3582
## ATOX1              562        973        481       1083        629        693
## FAXDC2            1892       5420       1392        570       3880       2366
## IL12B               15          4          4         62          0          4
## MIR146A              2          4          1          1          1          5
## PDLIM7             659       1206       1249        823        685       1756
## SERPINB1          1312       1675       1327      12365        942       1478
## SSR1              2364       4405       2375       2845       2233       3561
## CD83               344        326        146        520        147        317
## SOX4              1367       2417       1229        544        866       1525
## CMAHP              341        661        603        353        446       1250
## HLA-A            13250      23160      19255      26580      14280      25820
## HLA-C            18552      35094      10326      24547      13546      26260
## HLA-B            24886      37872      25595      42980      19577      32053
## MICA               362        704        697        492        363        619
## LTA                 26         53         27         24         18         51
## TNF                 98        118         66        132         60        104
## HLA-DRB1          4092       5805       3003      14947       6544       8924
## HLA-DQB1           513        856        605      11875       4929       2572
## PPARD              774       1956        900       2294       1114       1273
## CCND3             1039       2265       1337       1238        911       1629
## VEGFA             1347       2804       1185       1681       1590       1540
## RUNX2               92        218        191         84         99        178
## IL17A                0          0          0         59          0          0
## IL17F                0          0          0         42          0          0
## PRDM1              318        606        214       1536        644        530
## ATG5               723       1167        801       1335        787       1100
## TRAF3IP2           722       1431       1027        899        741       1119
## NCOA7              870       1277        739       1837        732       1385
## SGK1              2073       3468       2689       4575       1708       4118
## IFNGR1            3006       4451       2797       8653       2799       3750
## TNFAIP3            585        952        543        620        511        713
## SOD2              7764      11102       5321      20288       5060       6491
## LPAL2               12         18         15          6         13         21
## PLG                  2          5          1          0          3          2
## CCR6               134        232        123        127        100        154
## RAC1              5726       9682       6373       7028       5316       6685
## ZNF316             881       2525       1615        706        954       1729
## AHR               2696       4246       2804       2568       2461       3772
## IL6                  2          1          2         15          2          4
## TOMM7             3020       5609       3313       4013       3814       4974
## CYCS              3012       5071       3054       9926       3311       3393
## AQP1              4975      12390      12787       7040       6523      13183
## NT5C3A             746       1250        511       7276        897        734
## EGFR              3492       8397       6478       1649       4307       6677
## CD36              2986       5298       1417       6979       5307       5492
## SAMD9              177        303        192       1793        141        291
## SERPINE1           101         83         66        242         59         76
## CUX1               627       1500       1369       1115        853       1593
## PSMC2             2411       4154       2231       4866       2913       2886
## NAMPT             2955       4578       2050      20049       3093       3184
## HYAL4               36         28         71        523         17         66
## LEP                 27         36        154        124        275        576
## CALD1             3979       8197      10227       4417       4403      11298
## BRAF               436       1175        656        414        538        949
## EZH2               653        996        544       1034        444        719
## DNAJB6            2695       5952       2980      10732       3896       4072
## CSMD1               22         49         99          9         22         29
## CTSB              9408      16508       9291      19336      10703      15667
## EGR3              1180       2751        301        905       1887       1228
## TNFRSF10A          195        355        218        329        154        165
## BNIP3L            4040       8371       2177       8603       6987       4460
## DUSP4             1380       2290        424        373       1313        937
## NRG1                87        199        253        127        115        274
## RPL7             49602      91984      57569      63039      56871      66063
## IL7                103        191        172        188        134        271
## GEM                125        288        259        370        219        411
## MYC               1261       1867       1028       1195        928       1460
## GPT               1261       3451        317        195       2452        858
## JAK2               559       1167        755        769        554       1103
## CD274               98         81         60        466         44        103
## IL33               567       1161       2129       3659       1549       2626
## LURAP1L-AS1          3          4          2          0          3          3
## LURAP1L            257        571        390        540        286        648
## TTC39B            2406       4520        693       2875       3453       1428
## IFNA1                0          0          0          0          0          0
## TEK                180        414        419        153        203        495
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5              960       1468        818       2617       1188       1143
## ANXA1             5530      10183       8906      38829       6888      13711
## ERP44             1011       1757       1088       1424       1077       1320
## ZNF483             140        343        301         68        112        313
## TNFSF15             55        107         51         60         31         60
## TLR4               155        401        322        737        314       1249
## PTGS1             1832       4893       3730       2196       1804       4908
## HSPA5             8605      14740       6235       8734       9005       7695
## FNBP1             1379       2437       1911       1469       1275       2571
## CARD9               99        253        155        177        115        176
## TRAF2              447        886        541        322        384        527
## CLIC3              196        922        760       1688        563       1231
## IL2RA              109        101         49         87         21         98
## GATA3             2635       5137       3244        465       2053       3424
## VIM              16955      35374      29800      20240      22729      55494
## CREM               266        559        312        653        302        423
## DKK1                15         62        101         52         26         82
## MBL2                 0          0          0          0          0          1
## SAR1A             1877       3720       2129       2787       1963       3070
## PRF1                76        108         61        105         61        125
## ZMIZ1             1272       3684       2654       1225       1789       3286
## IFIT3              742        589        500       4173        381        828
## TALDO1            4526       8402       2397       5288       6594       3757
## IGF2               149        394        369        228        269        386
## INS-IGF2           143        378        356        214        258        377
## IGF2-AS              1          1          3          1          0          0
## INS                  0          0          0          0          0          0
## STIM1             1292       3567       2866       1369       1545       3193
## TRIM22            1336       1807       1143       3486        727       2217
## PTH                  0          0          0          0          0          0
## SAA1              4109       1739         92        609       1141        382
## SLC1A2              70        207        139         34         63        204
## FOSL1               20         37         19        139         18         28
## CCND1             2850       7742       6555       1216       3941       5938
## JRKL               202        450        378        133        201        413
## MMP7              1834       1883       1353       1235        339       1690
## MMP1                42          2          4       2152         13          6
## MMP3                11         15         75        203          2         36
## CASP1              837       1397        852       2937        929       1312
## DLAT               775       1604        949       1053       1065       1050
## IL18              1263       2108       1964       2231       1375       2515
## CD3E               302        400        183        259        192        296
## MCAM              2452       5166       3172       2032       2708       4264
## WNK1              2380       6630       4028       1976       3317       5706
## TNFRSF1A          2638       5284       3466       3265       2618       4253
## GAPDH            23044      47941      33788      41884      17720      32713
## CD4                683       1172        756        904        699       1793
## SLC2A3             380        471        307        936        220        720
## CLEC4D               2          3          0         32          1          2
## KLRB1               25         32         34        141         44         67
## CD69                72         81         36        207         48         61
## CLEC2B            1464       1573       2141       2724        884       2146
## OLR1                12         19          3         19          8          3
## ABCD2               32         32         41         29         31        137
## LRRK2              301        613        505        379        286        653
## VDR               1840       3423       1077        787       1555       1133
## TMBIM6           18914      38690      12902      15301      24708      17962
## PFDN5             5908       9495       5903      11452       6472       8232
## SP7                  0          2          3          0          2          1
## MUCL1             5535      18893      14013       1531       1942      10979
## CD63              8567      15285      12114      19256      10609      20195
## SUOX              1761       4203       1997       1170       2350       2507
## RPS26             5325       7246       8266      17915      11715       4053
## RPL41            61242      92147      56791     110931      67963      73395
## IL23A               13         22         17         63         10         18
## DDIT3              393        779        487        585        390        743
## IFNG                 5          4          0         40          6          0
## IL22                 4          2          0         67          0          0
## LYZ               3367       2675       2784       9558       2422       5210
## CAPS2               69        185        116         48         57        146
## SYT1                 9         32         31         10          7         67
## BTG1              5870      10780       5619       6184       4532       5922
## HCAR3              190        327        210       2323        136        294
## GJB2              4122       5090       2240      40229       3087       1923
## GJB6              2184       2885       2069      17704       1652       2003
## TNFSF11             43         64         13          2         27         15
## TPT1             83080     132476      86688     266201      98731     113773
## LMO7               527       1545        958       2281        681       1469
## TNFSF13B           233        223        138        547        194        336
## LAMP1             4414      11081       5262       3058       5708       6386
## PSME2             1871       2229       1308       3667       1375       1610
## GZMB                34         17          7        422         28         37
## RPL36AL           4313       6147       3566       5675       3687       4391
## PYGL               950       1560       1360       2319        983       1687
## HIF1A             1191       2884       2433       2987       1224       2345
## FOS                949        738        510        328        278        759
## JDP2               352        944        942        703        785       1775
## NOXRED1             37         50         51         20         22         44
## SERPINA1           154        251         47        879         86        141
## CDC42BPB          1329       3790       2614       1691       1928       3673
## PLA2G4D            320        559        199       5852        407        285
## TRIM69              29         55         38         47         13         36
## SLC51B              30         37         43         19         19         61
## SMAD3              907       2232       1317        656       1073       1727
## CYP1A1               6         51       2326          1          1         19
## AKAP13            1756       4338       2828       1337       2146       4202
## MEFV                 7         23         15         91         16         44
## SOCS1              114        219        112        251        135        121
## ATXN2L            1106       2632       1909        903       1199       2530
## CD19                 4          9          9          9         10          9
## ITGAL              351        471        227        232        188        374
## ITGAM              188        371        255        386        248        679
## ITGAX              306        447        250        796        179        676
## DNAJA2            1842       3561       2183       4598       1970       2924
## SIAH1              803       1414        984        686        680        923
## ADCY7              729       1637       1220        918        814       2372
## NOD2               489        766        344       1848        402        402
## CMTM2                9         14         10         19          8         16
## SF3B3             2334       4443       2586       2421       3086       3044
## PSMD7             2860       4873       2240       4195       3454       2844
## WWOX               205        385        235        282        231        296
## MAF               2402       5255       3937       1964       2560       5008
## SLC7A5            2224       4208       1507       1689       2253        926
## CXCL16             708       1202        697        904        640        882
## XAF1              1181       1086        981       1595        573       1306
## CD68               546        806        667       1774        615       2184
## PER1              1241       3652       4316       1801       3178       3912
## NOS2                 3         16          7        486         11         39
## TRAF4              921       2325       1043        994        886       1205
## CCL2               421        318        263        487        288        580
## CCL5               300        365         84        284        203        289
## CCL3                 7          3          3        518          7         19
## CCR7               194        100         66        192         36        188
## STAT3             5813      11756       5525      12651       5312       6661
## SOST                 0          3          2        372          2          2
## ITGA2B              12         36         18         16         17         57
## EFCAB13            110        182        167         35         53        167
## NPEPPS            1882       3912       2368       3252       2142       2996
## TBX21                5         24         12         13         21         15
## COL1A1           16216      51840      42677      26712     112739     162513
## MRPS23             875       1405        821       2228        948       1125
## MIR21                2          2          3          4          2          3
## RPS6KB1            674       1343        843        827        791       1078
## ACE                218        570        651        273        485        940
## ERN1               369       1031        592        507        434        753
## PRTN3                1          0          0          1          1          0
## PLIN5             2042       5181         95        969       4085        733
## RETN                 1          4          2          8          0          6
## CCL25                1          2          0          0          0          0
## ICAM1              496        660        511        861        445        920
## TYK2              1205       2982       1831       1153       1228       2619
## SMARCA4           1569       3899       2492       1285       1932       2674
## ACP5              1284       2732        413       2540       1579       1609
## JUNB              2847       4512       2589       7241       2599       2949
## CYP4F22            988       3131        311       2125       2392        970
## JAK3               256        334        163        299        143        349
## JUND              1470       3723       1990       1355       2332       2621
## CEBPA             4812      10002       3832       5920       6753       3869
## CEBPG             1267       2719       1828       2532       1461       1844
## ACP7               128        289         51       5329        533        273
## ZFP36              820       1415       1035       2324        838       1564
## TGFB1              623       1393        940        909        721       1754
## RPS19            23732      42429      26236      42132      24217      31118
## PSG2                 2          2          4          5          2          1
## FUT2               120        258        165        359         55        249
## NKG7                69        108         36        156         62         83
## ZNF415             197        474        254         76        133        178
## LILRB2             109        144         89        320        131        154
## LILRA5              15          8          4        138          6         24
## KIR3DL1              0          0          1          0          2          0
## KIR3DL2              0          2          0          1          1          2
## SMOX               112        452        151       1684        462        316
## BMP2               145        387        362        376        183        233
## GINS1              238        295        146        497        149        197
## PLCG1             1808       3650       2116       1859       1604       2765
## YWHAB             7790      13456       7848       7209       7778       9259
## PI3                224         54         48      57934        122         89
## MMP9               154        158         77        248        145        291
## CD40               455        605        452        435        375        575
## PFDN4              606        692        431       1124        468        568
## BMP7               444       1338        725        564        696        948
## RPS21            14029      18458      12505      26388      13560      14433
## MX1                878        808        697       2882        282        765
## PFKL              3720       9871       4103       2634       5096       5278
## IL17RA             844       1647        877        603        815       1176
## UBE2L3            2089       3614       1812       2973       2450       2332
## TPST2              459       1043        638        795        609        998
## XBP1              4130      10937       4924       6520       4610       5375
## UQCR10            1487       2618       1076       2228       1843       1580
## SEC14L2            532       1135        301        474        406        336
## APOL6             1121       1154        750       2571        619       1623
## APOL1              381        365        301       1354        369        422
## TYMP              2537       3148       1091      13928       2148       2093
## BEND2                0          0          2          0          1          1
## PHEX                15         44         18         74         15         38
## TIMP1              903       1498       1380       1664       1242       2607
## FOXP3              119        222         71        106         82        159
## MSN               3554       7083       5438       6692       4117       8264
## PGK1              8286      14504       7656      22293       8328       9929
## LAMP2             4487       8475       4168       5227       4912       5611
## CD40LG              62         81         50         23         26         56
## IRAK1             1957       4638       2328       2897       2267       2926
## COX2             31907      69863      38355      13776      44114      45829
##             GSM5629983 GSM5629984 GSM5629985 GSM5629986 GSM5629987 GSM5629988
## TNFRSF9            102         12         23         51         51         15
## ENO1             29875      15939      11718      18625      23955      13852
## PIK3CD             440        292        399        147        552        252
## PGD               3555       5560       1682       2576       3945       2986
## MTHFR              878        686        688        371       1273        474
## TNFRSF1B          1460        604        809        615       1176        590
## PINK1             1207       2614       1603       1130       2821       1337
## IFNLR1             240        135        290        105        504        135
## RUNX3              958        498       1198        470       1929        410
## SH3BGRL3          5313       3056       2817       3273       4032       2894
## CD52               498        167        212        604        230        269
## IFI6              6549        324        919       4446       1152        517
## ZC3H12A           6893       1955        824       1567       1096        773
## UTP11             1205        487        584       1188        755        563
## JUN               1334       1752       2314        947       2566       1413
## KANK4               11        176         65         51        100        106
## EFCAB7             145        137        138        197        261        139
## IL23R               10          7          5          7          0          5
## ADGRL2            1015       1675        830        484       1459       1015
## GBP3               838        170        329        918        735        445
## GBP1              5428        504        596       1512        717        528
## GBP5              1145         60        115        170        123        120
## TGFBR3            1231       1907       2654       1465       3827       1518
## VCAM1              605        398        340        778        516        439
## PTPN22             153         78         99         81        125         83
## CD160               22          8         21         15         23         10
## FCGR1A             209         12         12         85         16         10
## MCL1              7613       4217       6975       4072       7331       4088
## CTSK             11015       5874      15375      16726      16061      13147
## RORC               157       1166        574        118       1170        580
## S100A9          259724       9444       2632     276402        481      11129
## S100A12           1571         18          3        913          2          7
## S100A8          230363       7009       2061     325460        362      13818
## IL6R               691        541        914        425       1050        481
## RIT1               706        465        535        678        792        532
## BGLAP               15         16         16         10         42         13
## IFI16             7926       1386       2256       3305       3243       2026
## AIM2               351         13         20         92         31         10
## CRP                  0          0          1          1          0          0
## FCGR2A            1777        166        272        168        219        157
## HSPA6              420         72        171        156        151         63
## FCGR3A             631         48         76        304         34         47
## SELL               420         59         82        157        106         97
## GLUL             13425       9292       9001      13735      14400       9796
## PTGS2             1303         16         62         43         51         21
## CRB1                 5          7          3          2          9          6
## KDM5B             2016       1935       1596        984       2957       1717
## IL10                37          8         11         12          2          6
## YOD1              2554        737       1189        768        700        357
## HHAT               164        184        172         70        250        187
## TRAF5              295        215        399        238        424        238
## NLRP3              270         44        116         26         67         36
## LINC01250            0          0          2          2          0          0
## RPS7             23150      14016      12150      48820      21706      19163
## RSAD2              995         73         73        248        202         57
## FOSL2             5228       4684       5095       1216       7354       3086
## REL               1187       1005       1248        884       1668        798
## TGFA              2214       1150        610        690        714        551
## DYSF               415        271        309        232        735        185
## HK2               3685       3163        761        693       1737       1242
## CD8A               766        148        157        126        109         63
## CD8B               321         84         79         89         49         33
## EIF5B             4315       2746       3581       3863       6022       3249
## IL1R1             2645       1644       2251       1473       2893       1591
## RGPD6              306        345        550        246        790        287
## IL1A               407        107         26         14         42         67
## IL1B              5413        132         20         40         29         94
## IL37               159        352        841         49        480        213
## IL36RN            9822        732       1422       6378        942        454
## IL1F10              62         41         67         31         38         24
## IL1RN             7223       1069       1132       1263       1828       1123
## NMI               1655        346        327       1401        538        434
## TNFAIP6            387         55        244        118        124        119
## IFIH1             1381        271        518        782        692        371
## SCN1A                0          1          8          0         19          2
## ABCB11               9        115         20          3         66         44
## RBM45              214        119        154        176        234        141
## FRZB               380        359       1248        570       1859        602
## TFPI               476        317        615        817        820        465
## STAT1            11179       1531       2117       5234       2995       1756
## NABP1              688        273        237        274        290        238
## SF3B1             6760       5454       7048       4188      10427       4657
## CASP10             605        204        333        256        455        219
## CD28               189        101        104         86         68         72
## CTLA4              149         32         36         52         46         27
## ICOS               126         16         17         83         42         30
## NDUFS1            2637       4673       2062       2053       4232       2371
## CXCR2              531        122        106        244        117        169
## IRS1               415        788        902        273       1456        394
## CCL20               57         20         33        282         26         36
## ATG16L1            616        613        708        446       1078        403
## GPR35               23         35         53         18         71         16
## PDCD1               55         20         12         26         18         18
## PPARG              195        997        147        635        604        722
## RPL15            30460      23149      23114      53888      42002      30016
## EOMES               68         18         17         25         40         19
## CX3CR1              85        124        142        125        248        210
## ACKR2              302         18         29        145         31         28
## CCR2               241        150        192        267        280        315
## CCRL2              169         18         13         27         23         14
## TLR9                 8         18         16          3         32         10
## ARHGEF3           1154        525        807        743       1098        649
## ADAMTS9            177        175        270         81        391        170
## TMEM45A          11710      19115       6604      14374       8012      14504
## CD80                54          5         12         15          7          1
## CD86               312        102        171        203        201        125
## MIX23              332        164        151        504        250        171
## PLS1               139         70        141        124        256         86
## PTX3               198         18         61        127        120         38
## GOLIM4            1123       1018       1552        810       2618        881
## MYNN               684        465        577        738        749        391
## TNFSF10           4218        846       1194       4715       2502       1818
## ADIPOQ              70        695        478       4110       1992       1231
## SPON2              706        414       1334        607       1954        384
## S100P              568        153        281        492        643         81
## WDR1              9237       6542       5799       4406       7524       4164
## CD38                43          7         13         31         20          9
## PPARGC1A           130        691        512        121       1501        254
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          7         11          6          5          4
## CXCL8            27702         41          8        247          3          2
## CXCL2              304          9         18         44          7          3
## AREG               253        174        102        157        193        137
## CXCL10            2359         44         16        179         18         10
## CXCL13             493         20         18        451          4         42
## SPP1               239          7         56         22         59        100
## HERC6             1992        144        204        588        395        173
## NFKB1             2162       1191       1892       1216       2356       1013
## SEC24B             806        843       1032        730       1566        689
## EGF                 13         44        100         26        167         19
## IL2                  2          0          1          5          3          1
## IL21                17          1          0          1          0          0
## IL21-AS1             3          1          0          4          0          1
## SLC7A11            353         77         55        110         39         26
## IL15               149         43         93        166        130         95
## EDNRA              547        299        532        414        758        406
## TLR2               551        436        155        224        434        340
## FGB                  0          0          0          0          0          0
## DDX60             1819        422        745        893        859        492
## SPCS3             3246       2166       1935       3235       2571       1748
## TLR3               149         63        131        169        171        147
## OSMR              1433        835        895        529        990        554
## GZMK               219         36         53         65         56         59
## GZMA               340         39         63        322         99         35
## ANKRD55              3         11          8         17         16         14
## CENPK              274         81         78        203         81         67
## CAST              7781       6829       9079       4833      11216       5493
## ERAP1             2143       1874       2588       1597       3397       1961
## ERAP2             2531        937        147        117        195         95
## TNFAIP8           1264        556        632       1485       1121        835
## CSF2                14          7          6          7          1          2
## IL5                  2          2          2          0          5          0
## IL13                 4          0          0          0          0          0
## IL4                  0          0          5          0          2          0
## CD14              1876        701        823        827        860        368
## CSNK1A1          13238       5717       6868       8550       8464       5505
## PPARGC1B           413        480        333        245        588        385
## TNIP1             4364       2759       2389       2466       3785       1915
## ATOX1              769        419        388       1122        566        416
## FAXDC2             760       6749       1036        567       3008       2706
## IL12B               20          1          1         19         13          3
## MIR146A              1          0          1          4          3          1
## PDLIM7             981        735        993        725       1330        411
## SERPINB1          9427        764       1277       2460       1377        861
## SSR1              3619       2804       2548       2448       3801       2797
## CD83               442        177        278        401        445        222
## SOX4              1197        983       1194        546       2142       1181
## CMAHP              346        247        570        171        692        251
## HLA-A            21472       8592      17214      30711      27034      12763
## HLA-C            30502      11645      18638      31542      26325      12678
## HLA-B            46775      14887      22348      41564      35103      21407
## MICA               324        255        291        413        707        335
## LTA                 13         11         42          8         48         15
## TNF                169         45        111         37         59         31
## HLA-DRB1         12776       4899       4558       8231       6259       6209
## HLA-DQB1          9541       4070        934        732        887       1275
## PPARD             2722       1734       1177        766       1516        672
## CCND3             1376        999       1067        998       1480        778
## VEGFA             1387       1405        696        379       1868        850
## RUNX2              114         85        177         35        232        104
## IL17A               80          2          0          8          0          0
## IL17F               63          2          1         54          0          1
## PRDM1             1616        953        618        757        657        430
## ATG5               889        500        555       1155        879        607
## TRAF3IP2          1334        760        763        674       1361        799
## NCOA7             2837        722       1030        969       1162        674
## SGK1              5559       1499       2724       3079       5045       1608
## IFNGR1            5913       2242       2342       5119       3379       2819
## TNFAIP3           1828        577       1021        477        979        428
## SOD2             27605       5241       5199      11682       7111       4692
## LPAL2               11          7         15          2          8          6
## PLG                  2          0          2          1          5          2
## CCR6               108        121        223         57        145        188
## RAC1              8093       4614       5776       7442       8201       5352
## ZNF316             771       1098       1494        400       2196        620
## AHR               3423       2485       3369       3183       4491       2520
## IL6                158          3          3          6          8          3
## TOMM7             3158       2504       2413       6554       4441       2934
## CYCS              6944       3356       2244       7144       3743       2831
## AQP1              9838       5117      10542       8695      15669       5998
## NT5C3A            2289        767        586       2379        769        654
## EGFR              2778       4949       6088       1287      10687       3320
## CD36              3440       4565       1334       8367       2747       2794
## SAMD9             1599        164        251        256        288        262
## SERPINE1           526        135        424         67         93        142
## CUX1              1330        851       1394        754       1962        710
## PSMC2             3521       2371       2230       3895       2910       2233
## NAMPT            19581       2699       3363       6644       3079       2363
## HYAL4              135         14         26        155         32         11
## LEP                  2        108         89       1750        280        186
## CALD1             5397       4935       7804       7963      10602       4556
## BRAF               488        581        738        352       1128        503
## EZH2               818        392        453        603        691        323
## DNAJB6            7538       3632       3128       4681       3889       2740
## CSMD1                0         33         60         17         61         23
## CTSB             23498      17619      11564      11683      14342      11414
## EGR3               729       2897       1589        399       1836       1055
## TNFRSF10A          414        139        199        140        254        115
## BNIP3L            4459       6624       2840       4380       4441       4270
## DUSP4              655       1289        805        646       1587        553
## NRG1               343        136        289         49        373        137
## RPL7             44224      36426      33251      75682      64897      53076
## IL7                161         95        150        220        226        130
## GEM                446        173        385        455        399        235
## MYC               2319        843       1543       1095       1941        807
## GPT                102       3249        325        120       1622        964
## JAK2               815        476        842        635       1037        606
## CD274              882         50         70        161         65         35
## IL33              1851       1047       1433       2177       2197       1229
## LURAP1L-AS1          3          3          6          3          5          3
## LURAP1L            373        212        366        581        525        285
## TTC39B            1461       3623        961        995       1724       1789
## IFNA1                0          0          0          0          0          0
## TEK                297        179        344        261        537        203
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5             1456        759        669       2386        828        804
## ANXA1            36500       5300      10320       9918      11783       6736
## ERP44             1529        838        905       1358       1322       1021
## ZNF483              85         96        170         85        250        108
## TNFSF15             38         40         21         45        101         41
## TLR4               902        280        459        453        410        307
## PTGS1             2555       1661       4785       1694       4883       1682
## HSPA5            11937      10493       6257       7603      10016       7490
## FNBP1             1872       1327       2059       1247       2946       1047
## CARD9              116        152        177         63        173         78
## TRAF2              308        385        345        259        669        289
## CLIC3              913        560        839        805        954        427
## IL2RA              202         67        120         57         66         57
## GATA3              720       1588       3121        931       4767       1746
## VIM              23387      16357      34431      36769      44806      22200
## CREM               595        302        314        522        412        227
## DKK1                12         10         86         24        138         15
## MBL2                 0          0          0          0          0          0
## SAR1A             2460       1701       2254       2864       3463       1911
## PRF1               407         52         68        137        113         42
## ZMIZ1             1963       2439       2676        741       4311       1360
## IFIT3             3875        231        430       1467        700        360
## TALDO1            4141       4894       1880       3961       3939       3560
## IGF2               342        139        339        579        641        145
## INS-IGF2           318        126        309        567        592        137
## IGF2-AS              1          0          4          0          2          0
## INS                  0          0          0          0          0          0
## STIM1             1910       1632       2482        841       3723       1260
## TRIM22            3818        717       1568       1600       1466        890
## PTH                  0          0          0          0          0          0
## SAA1               570        610         51       4363        315       2227
## SLC1A2              33         70        117         46        128         68
## FOSL1              330         39        180         51         26         21
## CCND1             2250       4582       6446       1818       8983       3416
## JRKL               158        193        218        142        394        190
## MMP7               321        160        619        646       1518        331
## MMP1              1172         39         11         66          5         56
## MMP3                95          2         27         15         17         11
## CASP1             2226        655        828       1727       1186        967
## DLAT              1161       1202        739        853       1325        788
## IL18              1217       1055       1614       2093       1829       1670
## CD3E               577        222        233        245        267        294
## MCAM              2758       3206       2207       5754       4107       1680
## WNK1              3185       5053       5910       1602       7206       3186
## TNFRSF1A          4737       2495       3369       2436       4345       2012
## GAPDH            41908      17087      20077      34930      38333      20033
## CD4                973        837       1211        760       1466        954
## SLC2A3            2110        226        453        280        532        223
## CLEC4D              37          4          0          4          2          2
## KLRB1              134         34         32        145         51         82
## CD69               448         53        119        144         45         65
## CLEC2B             975        350        845       3312       1218        733
## OLR1               155          6          6         11          4         22
## ABCD2               23         52         48        173         59         71
## LRRK2              419        275        632        284        536        262
## VDR               1293       2366       1337        362       1937       1231
## TMBIM6           12545      26086      11097      12465      20893      15185
## PFDN5             5143       3206       3441      13042       5813       4924
## SP7                  0          1          9          0          6          2
## MUCL1             4079       2662       5375       1413      10709       2413
## CD63             11169       7816      10906      22446      14399      10461
## SUOX              1566       2478       1913       1104       3222       1729
## RPS26            10199       6994       1969      17946       9689      12911
## RPL41            54089      33667      30116     131780      53402      51696
## IL23A               44         11         19         12         18         14
## DDIT3              386        260        345        357        551        277
## IFNG                42          1          1          6          6          2
## IL22                91          0          1          5          0          0
## LYZ               8054       2918       2859      10922       3461       3306
## CAPS2               42         51         67         29        127         74
## SYT1                 2         20         35          3         33         25
## BTG1              6492       3132       3867       6421       6813       5256
## HCAR3             4463        191        212        474        411        160
## GJB2             50370       5171       2506       9787       3164       6385
## GJB6             15630       2040       1996       4043       2262       1958
## TNFSF11              8         25          1          6         13         22
## TPT1            108758      50898      52107     224029      81914      86674
## LMO7              1177        862       1258        945       1713        469
## TNFSF13B           348        150        173        446        223        238
## LAMP1             4632       6984       6200       2379       8578       4644
## PSME2             3445        957        959       3392       1550       1109
## GZMB               969         11         20         64         15         31
## RPL36AL           4858       2591       1973       6346       3412       3197
## PYGL              3493        986       1115       1969       1515        914
## HIF1A             5929       1632       2041       1376       3939       1248
## FOS                900        317        805        398        756        325
## JDP2               793        529       1673        703       1403        483
## NOXRED1             17         17         28         14         51         12
## SERPINA1          1276        151        156        310        217        161
## CDC42BPB          2181       2254       3202       1054       4371       1299
## PLA2G4D           6144       1451        349       1865        472        307
## TRIM69              31         19         14         23         22          6
## SLC51B              26         37         43         52         60         35
## SMAD3              896        794       1284        559       2005        805
## CYP1A1              25         83         10          2         92          9
## AKAP13            2268       2419       3797       1021       5133       1996
## MEFV               276          7         23         12         42          6
## SOCS1              404         76        173        126        224        109
## ATXN2L            1313       1267       1623        565       2776        864
## CD19                11          4          4          9         19          4
## ITGAL              456        269        267        165        284        212
## ITGAM              297        170        353        260        497        201
## ITGAX              661        160        423        125        482        182
## DNAJA2            3005       1853       2128       3337       2734       1729
## SIAH1              654        489        701        559       1096        561
## ADCY7             1073        891       1615        408       1691        639
## NOD2              1088        346        492        390        480        314
## CMTM2               19          4          4         16          9          3
## SF3B3             2892       2948       2395       1563       4281       2273
## PSMD7             3154       2801       1877       3369       2931       2177
## WWOX               113        119        218        131        232        213
## MAF               2931       2127       4266       2184       5465       2196
## SLC7A5            4218       3736        929        740       1600        771
## CXCL16            1449        852        705        565       1003        656
## XAF1              2165        297        806        683        923        379
## CD68              1627        607       1081       1293       1097        658
## PER1              2656       2706       5892       1230       7227       1971
## NOS2               991          7         32         15         42          6
## TRAF4              823        657        839        551       1492        397
## CCL2               951        137        322        600        284        212
## CCL5               708        127        179        367        275        203
## CCL3               359         10          9         28          4          7
## CCR7               375        124         86        249        178        135
## STAT3            13310       6699       5917       4902       9534       4918
## SOST                76         27         97         12          4          0
## ITGA2B              24         18         21         18         28          4
## EFCAB13             39         53         80         37        149         56
## NPEPPS            3425       2106       2029       1650       3259       1536
## TBX21               21         17          9          2         17          9
## COL1A1           56608      46382     132174       8619     158539      78663
## MRPS23            1135        595        561       1859        925        633
## MIR21                2          0          1          2          1          1
## RPS6KB1           1044        749        937        662       1187        630
## ACE                582        364        800        284       1020        229
## ERN1               503        615        647        252        974        370
## PRTN3                1          0          0          0          2          0
## PLIN5              437       4970         72        224       1430        998
## RETN                31         19          3         10          3          1
## CCL25                2          2          0          0          1          0
## ICAM1             2754        425        847        360        829        355
## TYK2              1261       1107       1649        590       2371        721
## SMARCA4           1898       2251       2227        784       4048       1399
## ACP5              1406       1658        635        966       1288        985
## JUNB              5746       3195       2358       2165       3355       1547
## CYP4F22           1572       3450        831        784       1850       1210
## JAK3               539        221        219        119        331        145
## JUND              2146       2450       4343       1141       3698       1211
## CEBPA             4421       7223       4690       5265       6207       3620
## CEBPG             2055       1243       1769       1624       2368       1192
## ACP7              2634       1355        245        868        255        252
## ZFP36             5160       1016       1568        665       1848        620
## TGFB1             1531        728       1402        802       1389        654
## RPS19            25908      14487      15763      42926      27544      19306
## PSG2                 1          0          1          1          3          3
## FUT2               422        107        128        189        247         73
## NKG7               258         56         42        148         75         43
## ZNF415              76        135        119         88        265        181
## LILRB2             376         62        123        125         81         41
## LILRA5             187          7          7         31          4          3
## KIR3DL1              0          0          0          0          0          0
## KIR3DL2              3          0          0          0          0          4
## SMOX              1346        835        353        277        428        182
## BMP2               612        195        598        168        479        214
## GINS1              340        144        141        403        207        140
## PLCG1             1826       1621       2003        827       2970       1017
## YWHAB             9517       7984       6484       7514      10565       7348
## PI3              45827       2487         81      14188         85        727
## MMP9               324        332        132        278        147        140
## CD40               601        247        431        586        557        244
## PFDN4              491        234        274       1257        424        399
## BMP7               670        676        759        412       1170        393
## RPS21            12137       6122       5740      34443      10986      10466
## MX1               5529        384        476        867       1015        309
## PFKL              3162       4300       3969       1815       6480       2849
## IL17RA             764        879        918        330       1239        619
## UBE2L3            2809       1966       1629       2604       2535       1818
## TPST2              811        496        852        574       1100        445
## XBP1              5441       5643       4628       4705       5778       3115
## UQCR10            1401       1352        661       1978       1377       1084
## SEC14L2            559        540        341        181        566        507
## APOL6             3138        511        812       1609       1204        654
## APOL1             2380        229        305        435        417        273
## TYMP             16860       2857       1428       4108       2010       1782
## BEND2                0          1          0          2          1          0
## PHEX                54         20         25         30         48         14
## TIMP1             1633       1224       1812       1518       2232       1432
## FOXP3              155         99        109         64        146         75
## MSN              10103       5060       6937       5631       8137       4851
## PGK1             15000       8126       6431      15660       9491       7760
## LAMP2             4552       4562       4268       4117       6334       4632
## CD40LG              20         41         32         36         54         51
## IRAK1             3479       2741       2576       1724       3269       1534
## COX2             14627      30865      29169      28465      68381      30865
##             GSM5629989 GSM5629990 GSM5629991 GSM5629992 GSM5629993 GSM5629994
## TNFRSF9             22         18          9         47         29         38
## ENO1             17723      21601      15229      20754      19095      24675
## PIK3CD             165        152        164        287        463        363
## PGD               2640       4366       5215       2469       3655       2800
## MTHFR              366        267        326        806        898        739
## TNFRSF1B           422        371        401        773        949        902
## PINK1              775       1706       1435       1152       2649       1365
## IFNLR1             149        120        120        257        266        210
## RUNX3              383        730        418        715       1052        463
## SH3BGRL3          1769       2500       2460       3921       3663       4584
## CD52               405        263        152        249        225        331
## IFI6             13438        769        497       2147        607       8260
## ZC3H12A           2333        373        560       3862        838       4134
## UTP11             1313        804        517        807        729       1174
## JUN                505        948        692        943       1743       1135
## KANK4               13         73        152         15        101         31
## EFCAB7             143        159        137        114        190        125
## IL23R                6         11          5          6         10          8
## ADGRL2             492        834        476        680       1198        812
## GBP3               766        380        143        721        505        939
## GBP1              1011        438        241       1189        541       1695
## GBP5               170         27         39        238        149        188
## TGFBR3             725       1607       1942       1277       2480       1304
## VCAM1              277        484        158        270        454        607
## PTPN22              76         42         50         73        119         87
## CD160                3          3          7         11         16         16
## FCGR1A              17          5          7         23          4         81
## MCL1              5043       4004       2521       4191       4600       5772
## CTSK              6387       7690       8968       8406      14062      10665
## RORC               147        645        593        118        976        194
## S100A9          389117       4195        478     210657       6756     285663
## S100A12           2275          7          1       1057          3       1197
## S100A8          526708       5374        626     195026       5733     256069
## IL6R               470        330        339        447        741        626
## RIT1               918        597        372        630        673        746
## BGLAP               13         15          8         15         14         12
## IFI16             5065       1612       1127       4331       2483       5656
## AIM2                45         15          2         31         14         95
## CRP                  6          1          1          0          0          1
## FCGR2A             117         97         89        265        230        349
## HSPA6              123         97         39        246        130        248
## FCGR3A              65         17         31        116         66        397
## SELL               212         37         32         99         68        186
## GLUL             12046      10945       7668      13627      11979      15096
## PTGS2              106         14         21         51         50         70
## CRB1                 0          3          1          2          3          2
## KDM5B             1488       1216       1456       1694       2537       1653
## IL10                12          6          2         16         13         34
## YOD1              1391        569        242       2597       1076       2142
## HHAT               139        195        143        199        215        173
## TRAF5              100        104         87        159        311        180
## NLRP3               24         23          9         48         64         88
## LINC01250            0          0          0          0          0          0
## RPS7             43909      34935      22944      21835      18365      32420
## RSAD2              645         96         50        142        110        933
## FOSL2             1452       2307       2234       4636       4742       4437
## REL               1070        527        560       1955       1135       1304
## TGFA               849        635        503       1088        914       1260
## DYSF               101        235        189        331        321        378
## HK2                786        739        854       2825       2083       2498
## CD8A               313        198         75        193        123        188
## CD8B               106        103         37        111         41         53
## EIF5B             3218       3235       3655       3867       3808       3790
## IL1R1             1621       1426       1083       2028       2558       2125
## RGPD6              186        184        153        258        460        241
## IL1A                48         30         16         15         63         12
## IL1B               163         40         31         76         52         71
## IL37                65        376        140        222        981        170
## IL36RN            5327        593        200       8854       1052       8249
## IL1F10              28         48          7         30         91         40
## IL1RN             2222       1813       1186       1944       1284       1909
## NMI               1602        510        297        967        417       1344
## TNFAIP6             66         75         41         83         59         90
## IFIH1             1158        326        229        600        494       1052
## SCN1A                0          0          1          1          5          0
## ABCB11              11         50         57          6         39         22
## RBM45              144        116        118        144        164        176
## FRZB               359        884        519        285        710        460
## TFPI               492        453        374        381        571        645
## STAT1             5177       1903       1351       4526       2250       5741
## NABP1              419        115         68        294        282        399
## SF3B1             3975       3205       2820       5039       6579       5107
## CASP10             383        155        157        304        306        343
## CD28               100         30         26         95         96        166
## CTLA4               59          7          2         75         18         50
## ICOS               103         17          5         44         30         53
## NDUFS1            2395       2641       2658       2254       3948       2644
## CXCR2              360        107        103        340        214        301
## IRS1               126        467        419        465        840        304
## CCL20              159         11          4         49         28         62
## ATG16L1            448        414        349        424        795        556
## GPR35               13          6          9         19         40         27
## PDCD1               38          5          9         21         33         29
## PPARG              161        746        981        127        678        378
## RPL15            43907      53145      34352      27500      32564      41206
## EOMES               15         10         16         15         27         42
## CX3CR1              87         78        113         75        239        177
## ACKR2               60         23         27        181         40        246
## CCR2               204        209         87        148        368        391
## CCRL2               33         12         16         27         14         27
## TLR9                12          2          5          9         17         17
## ARHGEF3            962        645        438        793        793        994
## ADAMTS9             65         98         85         93        165        176
## TMEM45A          12168      14172       9160      13508      14337      15068
## CD80                15          4          3         13          5         10
## CD86               127        129         75        168        168        249
## MIX23              423        228        190        244        224        344
## PLS1               189        153         71        145        129        124
## PTX3                37         20         22         32         39        117
## GOLIM4             468        797        587       1024       1452        986
## MYNN               797        627        358        491        585        656
## TNFSF10           5241       1609       1087       2641       2038       4218
## ADIPOQ             277        130        218        340       1051       1725
## SPON2              166        508        402        608        854        846
## S100P              685        313        105        711        295        514
## WDR1              3553       5608       4009       5934       6611       6857
## CD38                32          6          4         32         18         30
## PPARGC1A           130        610        387        161        498        140
## TMPRSS11B            1          0          0          0          0          0
## CSN3                 0          0          0          0          2          0
## ALB                  0          0          2          0          2          0
## CXCL8             2568          6          0        944          0        837
## CXCL2               26          6          0         50          7         77
## AREG               235        146         54         89        113         65
## CXCL10             121         13         34        188         20        193
## CXCL13              82          8          3        140         16        180
## SPP1                15         29         29         32          8        170
## HERC6             1848        161        141        550        222       1444
## NFKB1             1267        907        730       1665       1688       1640
## SEC24B             793        671        669        775       1110        662
## EGF                 18         60         38         16         63         16
## IL2                  5          2          1          0          1          0
## IL21                 5          0          0          2          0          5
## IL21-AS1             3          0          0          5          0          1
## SLC7A11            249         19         14        291         62        223
## IL15                68         66         40         79         75         66
## EDNRA              331        311        176        321        397        484
## TLR2               189        146        113        207        480        327
## FGB                  0          0          0          0          0          0
## DDX60             1186        349        203        776        768       1350
## SPCS3             2951       2675       1632       2324       2294       2739
## TLR3               126         95         76        141        156        186
## OSMR               625        411        236        991        897       1087
## GZMK                37         23         24         26         70         78
## GZMA               172         40         38         97         68        199
## ANKRD55             19          5          3          1          7          5
## CENPK              210         76         33        182         81        194
## CAST              5689       6589       4762       6994       8720       6946
## ERAP1             1626       1892       1825       1900       2543       1860
## ERAP2               93         51         36        999        909       1081
## TNFAIP8           1625        901        630       1090        965       1199
## CSF2                16          2          2          0          3          8
## IL5                  0          0          0          1          2          0
## IL13                 7          5          1          3          3          3
## IL4                  1          0          1          1          2          0
## CD14               364        477        398        814        855       1663
## CSNK1A1           9019       7265       4107       9920       6704      12188
## PPARGC1B           194        130        115        532        495        393
## TNIP1             1776       2115       1476       3198       3538       3827
## ATOX1             1190        677        426        686        493        880
## FAXDC2             591       1392       1771        753       3920        830
## IL12B               17          3          0         13          1          4
## MIR146A              2          0          0          6          1          5
## PDLIM7             264        456        340        486        725        848
## SERPINB1          2620       1033        780       2381       1065       2394
## SSR1              2925       3465       2588       2713       3201       3340
## CD83               340        159         99        278        263        213
## SOX4               643        773        890        694       1706        731
## CMAHP              121        172        185        145        315        148
## HLA-A            13119      13439      11472      13646      14936      19872
## HLA-C            17683      19988      11390      18243      21018      25553
## HLA-B            22771      22888      16402      20698      21321      33031
## MICA               264        201        194        250        367        322
## LTA                  8          4          6         17         28          8
## TNF                 40         38         18         59         65         55
## HLA-DRB1          4152       4070       2876       3716       3915       7716
## HLA-DQB1           483        574        399        441        616       1463
## PPARD              601        717        705       2296       1474       2048
## CCND3             1177       1089        898        896       1249       1210
## VEGFA              291        361        434       1173       1126       1041
## RUNX2               43         56         30         93        138         69
## IL17A               49          0          0          8          0         15
## IL17F               34          2          0         16          1         33
## PRDM1             1011        304        163       1630        791       1508
## ATG5              1000        913        542        640        700        926
## TRAF3IP2           599        881        583        930        942       1079
## NCOA7             1185        623        543        932       1091       1232
## SGK1              3815       1752        848       2761       1791       3808
## IFNGR1            4339       2789       1442       2950       2735       4553
## TNFAIP3            183        373        156        532        599        407
## SOD2              9900       7093       4170       9195       8981      10554
## LPAL2                5          1          1          3         13          7
## PLG                  1          0          1          2          3          2
## CCR6               105        137        125         66        233         87
## RAC1              8562       7688       5764       6581       6234       7238
## ZNF316             173        346        368        804       1252        675
## AHR               2809       2095       1210       2596       3115       3079
## IL6                  0          0          5          0          1          9
## TOMM7             4607       6408       4196       2902       3736       3526
## CYCS              6910       4368       3184       4227       3326       6041
## AQP1              4573       8811       9013       6112       8991      11429
## NT5C3A            2944        830        538       3208        907       2773
## EGFR              1494       2671       2934       3789       5772       2629
## CD36              5037       2175       1511       5458       2283       8622
## SAMD9              797        162        141        500        333       1060
## SERPINE1            78        118         38        115         60        223
## CUX1               606        944        750       1321       1311       1408
## PSMC2             3452       3120       2030       2664       2746       3284
## NAMPT             8973       3296       1926       8038       3030       9235
## HYAL4              374         30          1        218         31         98
## LEP                 30          6         53         35        180        823
## CALD1             2827       4944       4468       3731       7075       6857
## BRAF               271        306        323        481        689        437
## EZH2               653        228        186        594        375        636
## DNAJB6            4755       4342       2836       5394       3875       6664
## CSMD1               11         16         27          1         39         21
## CTSB             11341       8801       5150      13734      14526      27791
## EGR3               432        889        912        835       1696        738
## TNFRSF10A          223        134         94        201        170        234
## BNIP3L            4447       4437       4592       4421       5646       5003
## DUSP4              176        509        914        339        913        375
## NRG1                35        207         55         88        170        134
## RPL7             62834      84934      64557      38642      49822      59560
## IL7                125        149         82        131        124        174
## GEM                167        180        123        183        294        322
## MYC               1536        932        628       1020       1174       1574
## GPT                 97       1253       1936        189       1812        205
## JAK2               656        450        333        600        813        592
## CD274              251         27          8        156         59        204
## IL33              2515       1296        918       1443       1145       1947
## LURAP1L-AS1          2          3          2          2          3          5
## LURAP1L            387        419        177        275        381        446
## TTC39B            1583       1694       2001       1327       2542       1325
## IFNA1                0          0          0          0          0          0
## TEK                157        206        173        183        284        403
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5             1785       1445        959       1124        777       1506
## ANXA1             6700       8635       5136       7193       6883      10696
## ERP44             1195       1154        826       1076       1057       1244
## ZNF483              47         53         59         60        171         65
## TNFSF15              8         23         27         26         65         13
## TLR4               184        241        168        493        617        617
## PTGS1             1987       1929       1918       3364       3619       3312
## HSPA5             7503       8661       8463       8592       9861       9636
## FNBP1              888       1003        799       1704       1924       1508
## CARD9               70         76         28        126        131        158
## TRAF2              346        306        225        284        452        354
## CLIC3              996        848        305       1144        841       1240
## IL2RA               66         41          8         73         48         82
## GATA3             1350       2175       2762       1286       2993        922
## VIM              14352      23942      18920      23799      28072      27984
## CREM               397        404        254        234        331        351
## DKK1                14         25         24         36         17         41
## MBL2                 0          0          0          0          0          0
## SAR1A             2206       2119       1677       1736       2096       2303
## PRF1                87         27         27         64         82         95
## ZMIZ1              442        963       1079       1856       2535       1489
## IFIT3             1788        345        298       1007        382       2494
## TALDO1            4147       5495       5505       3423       3949       4146
## IGF2                60        273        245        270        301        657
## INS-IGF2            56        266        236        254        280        588
## IGF2-AS              0          0          1          0          0          1
## INS                  0          0          0          0          0          0
## STIM1              860       1671       1356       1763       2293       1828
## TRIM22            2115        547        315       1487       1032       2139
## PTH                  0          0          0          0          0          0
## SAA1              1189       1376        784        270        647       1263
## SLC1A2              24         22         21         21         64         32
## FOSL1               87         77          6         91         17        104
## CCND1              976       2945       3513       1555       5616       1961
## JRKL               119        137        130        102        330        168
## MMP7               530        766        498        672        817        349
## MMP1                 8          3          6         17         13         35
## MMP3                 3          6          6          8         20         57
## CASP1             1799       1017        474       1386        852       1553
## DLAT               803        978        862        809       1164        950
## IL18              2474       2334       1280       1710       1898       1800
## CD3E               347        205        170        214        318        226
## MCAM               906       2016       2408       1403       3035       3829
## WNK1              1280       2477       2184       4094       5743       3362
## TNFRSF1A          2966       2767       2284       2861       3269       3749
## GAPDH            35817      32991      21462      28214      26668      41644
## CD4                398        673        479        974       1288       1254
## SLC2A3             293        247        149        267        335        375
## CLEC4D               3          0          1          1          0          5
## KLRB1              151         93         36         70         99        123
## CD69                74         51         26         58         62         87
## CLEC2B            2855        898        811       2045        911       2950
## OLR1                 5          3          3          9         16          4
## ABCD2               20         11         13         39         74         78
## LRRK2              159        163        108        277        466        252
## VDR                568       1029       1301        823       1662        794
## TMBIM6           11920      24829      23794       9859      20884      14266
## PFDN5             8470       8322       5210       4543       4602       7178
## SP7                  0          2          5          0          0          1
## MUCL1             2835       6819       7282       1532       4698       3594
## CD63              9427      14807       9719       9781      11730      14760
## SUOX              1084       2144       1988       1338       2587       1466
## RPS26            21274      21674      10424       8357       8087      17646
## RPL41           102119     103528      63206      51378      49934      80906
## IL23A               12          5          5         19          7         19
## DDIT3              376        225        221        296        329        286
## IFNG                 7          0          3         11          2          4
## IL22                16          0          0          1          1          8
## LYZ              10225       4908       1662       6792       3693       8703
## CAPS2               20         56         40         44         80         29
## SYT1                 3         14          6         25         43          6
## BTG1              8609       5369       4742       5298       5208       6262
## HCAR3              423        193        136        451        193        381
## GJB2             21045       2701       1235      23164       5432      30694
## GJB6              6192       1454        658       7651       2132       9672
## TNFSF11             15         18         11          9         17         11
## TPT1            180074     149551      92372     100663      80922     150615
## LMO7               857        625        491       1653       1140       1330
## TNFSF13B           200        195        102        239        199        321
## LAMP1             2316       5424       6263       5294       7230       5102
## PSME2             2489       1531       1021       1742       1163       2577
## GZMB               221         16         10         97         18        153
## RPL36AL           6600       5729       3675       3232       3065       4314
## PYGL              1917        930        667       2183       1169       2899
## HIF1A             1828       1687       1344       2030       2285       2741
## FOS                257        300        268        292        783        375
## JDP2               434        651        401        673        845        780
## NOXRED1              9          8          6         15         33         12
## SERPINA1           253         60         44        282        139        452
## CDC42BPB           566       1106       1016       2519       2738       2164
## PLA2G4D           3666        169         85       6630        727       5880
## TRIM69              10         10          5         19         29         28
## SLC51B              14         16         18         19         39         31
## SMAD3              516        532        769       1000       1474        864
## CYP1A1             210        369         14          0        115          3
## AKAP13             577       1262       1217       2289       3305       1726
## MEFV                26          7         10         17         18         47
## SOCS1              135         79         73        101        107        135
## ATXN2L             390        476        412       1110       1746        980
## CD19                12          2          2          2         10          4
## ITGAL              132         65         76        205        362        207
## ITGAM               86        188        114        323        360        317
## ITGAX               79         55         19        149        180        181
## DNAJA2            3102       2116       1474       2186       2195       2751
## SIAH1              452        436        374        586        610        534
## ADCY7              271        320        293       1215       1521        922
## NOD2               503        258        127        968        510       1196
## CMTM2                8          0          3          2          5          4
## SF3B3             1826       2273       2035       2375       3078       2589
## PSMD7             3217       3172       2510       2680       2687       3081
## WWOX               400        239        183        164        189        323
## MAF               2176       1707       2103       3626       4213       3565
## SLC7A5            2005       1713       1344       2909       1458       2024
## CXCL16             528        718        454        762       1085        793
## XAF1              1326        173        153        852        495       1347
## CD68               698        632        394       1519       1177       1810
## PER1               485       1346        895       2694       1964       1644
## NOS2                97          4          2        230          9         91
## TRAF4              548        507        478        497        814        615
## CCL2               347        133         94        242        295        593
## CCL5               182         90        133        158        143        164
## CCL3                44          1          2         55          7         14
## CCR7               147         36         29        106         97        144
## STAT3             5696       5225       3939       8801       7211       8622
## SOST                19          1          0         27          0         63
## ITGA2B               7          8          6          8         14         22
## EFCAB13             12         19         21         45         95         32
## NPEPPS            1481       1389       1048       1904       2177       2184
## TBX21               11          6          2         15         10         17
## COL1A1            6893      21806      37203     137114      65821      98470
## MRPS23            1345        926        688        863        744       1153
## MIR21                1          1          1          0          1          1
## RPS6KB1            683        649        508        763        946        916
## ACE                141        260        263        508        396        659
## ERN1               206        220        232        490        663        379
## PRTN3                1          0          1          0          0          0
## PLIN5              272        608       1020        480       2043        483
## RETN                 0          3          2          0          4          2
## CCL25                0          0          0          0          0          1
## ICAM1              325        265        332        449        519        558
## TYK2               393        387        296       1029       1464       1029
## SMARCA4            785       1217       1499       2232       2346       1704
## ACP5              1041       1138        830       1650       1102       1711
## JUNB              3543       2083       1082       3227       2771       4821
## CYP4F22            928       1250       2074       2196       2345       1790
## JAK3               100         49         50        180        203        227
## JUND               594       2089       1414       1710       2198       1530
## CEBPA             5038       5631       4895       5211       5760       5267
## CEBPG             1915       1602       1078       1544       1506       1857
## ACP7              1279        135         63       3029        843       3021
## ZFP36              804        487        375       1422        924       1327
## TGFB1              564        671        575        886       1214       1164
## RPS19            35230      33195      23210      20140      20653      33149
## PSG2                 1          3          0          5          9          4
## FUT2               385         64         49        378        130        337
## NKG7                35         14         39         45         41        106
## ZNF415              94        162        129         53        147         96
## LILRB2              51         27         26        148        106        168
## LILRA5               7          3          0         22          2         27
## KIR3DL1              2          0          1          0          2          0
## KIR3DL2              2          0          1          0          2          0
## SMOX               360        224        107       1021        558       1221
## BMP2               200        301        150        192        218        268
## GINS1              461        158        101        211        179        308
## PLCG1              764        581        628       1879       2189       1612
## YWHAB             8282      10589       9261       7801       9021       8924
## PI3              42807        161         38      26360        441      25482
## MMP9               126         92         99        316        355        365
## CD40               338        397        218        367        337        445
## PFDN4             1147        566        434        510        324        700
## BMP7               532        647        564        697        795        699
## RPS21            24778      21814      13710      12105       9445      17933
## MX1               2311        295        230       1589        564       3445
## PFKL              1352       2893       3131       2983       5147       3118
## IL17RA             267        412        515        585        957        630
## UBE2L3            2550       2389       1918       1975       2000       2467
## TPST2              544        491        296        711        657        725
## XBP1              3812       5514       4210       4037       5772       5057
## UQCR10            1984       1889       1607       1047       1264       1567
## SEC14L2            277        361        212        324        592        369
## APOL6             1155        381        467       1302        856       1847
## APOL1              740        131        142        922        333        979
## TYMP              4799       1591        931       5752       2427      10372
## BEND2                4          0          0          0          0          0
## PHEX                59         19          9         62         25         20
## TIMP1              863       1211       1147       1158       1528       2270
## FOXP3               62         48         52        100         97        110
## MSN               3868       5913       3318       7029       7330       8603
## PGK1             12987      10277       6596      10705       9414      13961
## LAMP2             5325       6208       4424       3936       5384       4688
## CD40LG              36         35         26         17         82         34
## IRAK1             1233       1666       1672       2956       3194       2826
## COX2             15067      25537      30774      41964      39726      22822
##             GSM5629995 GSM5629996 GSM5629998 GSM5629999 GSM5630000 GSM5630001
## TNFRSF9             37         10         16         16         96         14
## ENO1             23460       8939      10057       9220      18420      15653
## PIK3CD             423        278        321        187        267        327
## PGD               3877       1730       1691       2166       2915       2151
## MTHFR              722        634        691        449        591        631
## TNFRSF1B          1053        600        730        629        753        772
## PINK1             2827       1429       2512       1660        735       1632
## IFNLR1             231        221        164        184        203        276
## RUNX3             1073        439        549        526        456        822
## SH3BGRL3          4440       2552       2672       2300       3478       4239
## CD52               346        188        222        167        233        217
## IFI6              1348        695        468       1008       3464        748
## ZC3H12A           1056        412        299        240       4680        559
## UTP11              816        576        640        582        906        586
## JUN               2286       1445       1243       1178        824       1355
## KANK4              135         79         45         59         16         75
## EFCAB7             178        150        139        105         96        162
## IL23R                4          1          1          1          6          3
## ADGRL2             997        968        808        839        806        939
## GBP3               600        280         59         39        741        476
## GBP1               649        428        321        576       1314        436
## GBP5               187         77        160         89        287         76
## TGFBR3            2734       1876       2924       2266        704       2968
## VCAM1              623        355        180        321        364        406
## PTPN22              83         45         43         23        110         57
## CD160               25         14         13         11         10         10
## FCGR1A              33          4         11         11         43          6
## MCL1              6052       4251       3465       4292       6547       4870
## CTSK             14052      14545      26865      11720       6228      13603
## RORC               724        462        793        602         95        578
## S100A9            5435       1109        201        234     237778        935
## S100A12              6          4          0          1       1818          1
## S100A8            4960        799        132        269     217804        802
## IL6R               773        520        642        449        512        626
## RIT1               739        467        535        505        612        465
## BGLAP               22         29         10          7          6         20
## IFI16             2254       1750       1972       2313       4781       2425
## AIM2                23         14         15          7         37          5
## CRP                  0          0          0          0          0          0
## FCGR2A             220        146        202        141        360        142
## HSPA6              118         82         98        113        122        133
## FCGR3A             174         52         53         36        200         32
## SELL               133         65         35         44        207         24
## GLUL             12409       9392      10631       8371      19868      11183
## PTGS2               33         27         40         55        237         13
## CRB1                 6          2          4          1          3          3
## KDM5B             1873       1605       1287       1451       1676       1855
## IL10                17          6         22          2         17         11
## YOD1               862       1108        874       1178       1691       1078
## HHAT               161        125        135        131         95        133
## TRAF5              312        244        219        130        137        237
## NLRP3               73         30         40         24         60         31
## LINC01250            0          0          0          0          0          0
## RPS7             32566      20942      26657      19503      18927      19351
## RSAD2               88         82         54         87        515        106
## FOSL2             3943       3202       3148       4580       3397       4352
## REL                853        773        852        912       1313        800
## TGFA              1054        953        714        594       2714        576
## DYSF               369        227        249        312        254        350
## HK2               1444        822        522        718       2972        811
## CD8A               148         63         75         54        236         86
## CD8B                59         39         25         46         79         62
## EIF5B             3849       3424       3269       3904       2971       3688
## IL1R1             2222       1949       2698       2011       1855       2392
## RGPD6              417        449        440        296        234        499
## IL1A                50         40         24         39        140         78
## IL1B                23         14          8         14       1012         11
## IL37              1033        809       1110        988         23        776
## IL36RN            1031       1065       1034       1439      17388       1300
## IL1F10              76        100         84         50         45        101
## IL1RN             1488       1382        991       1393       4886       1445
## NMI                563        430        364        420        723        459
## TNFAIP6             83         56        212         88        190         81
## IFIH1              497        416        350        445        674        402
## SCN1A                3         10          4          8          1          2
## ABCB11              50         22         65         56         12         34
## RBM45              144        130        130        106        156        141
## FRZB              1929        764        650        392        129        510
## TFPI               666        656        756        572        338        667
## STAT1             2546       1619       1505       2767       4629       2092
## NABP1              275        253        272        105        498        204
## SF3B1             6142       5140       5898       4031       4274       5661
## CASP10             326        249        242        275        392        268
## CD28               111         59        100         31        126         61
## CTLA4               56         21         27         26         82         28
## ICOS                50         12         30         21         70         10
## NDUFS1            3646       1849       1838       1970       2473       2314
## CXCR2              191        114         39         86        648        108
## IRS1               616        634        671        684        322        788
## CCL20               52         45          4          3        274         24
## ATG16L1            838        461        641        456        498        572
## GPR35               44         26         36         10         34         39
## PDCD1               39         13          7          6         49          7
## PPARG              708        430        488        384        148        356
## RPL15            50918      33420      38026      32289      24092      33050
## EOMES               60          6         13          8         35          7
## CX3CR1             240         88        110         89         90         81
## ACKR2               32         19         36         23        360         32
## CCR2               430        185        241        105        247        211
## CCRL2               36         10         17         22         49         22
## TLR9                28          8         16          2         17         24
## ARHGEF3            859        633        755        732        677        740
## ADAMTS9            145        234        136        212        121        272
## TMEM45A          15918       7116       9572      11341      14853       7588
## CD80                12          2          3          5         31          4
## CD86               214         90        154         79        173        134
## MIX23              220        187        197        160        309        179
## PLS1               142         67        105         92        202        149
## PTX3                83         56         42         53         96         53
## GOLIM4            1349       1267       1140       1035        832       1705
## MYNN               658        508        531        480        511        527
## TNFSF10           2162       1874       1795       1299       2834       1823
## ADIPOQ             577       1979        671        721        153        598
## SPON2             1021        914        918        587        245       1177
## S100P              334        541        705         78        749        405
## WDR1              7228       4393       4500       4824       6215       5784
## CD38                27          7         10          5         42          3
## PPARGC1A           851        221        399        164        166        497
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  8          7          0          2          1          0
## CXCL8                4          0          5          0       6267          3
## CXCL2                7          5          8          6         93          4
## AREG               249         82         45         31        278         79
## CXCL10              64         11          1         15        178          1
## CXCL13              22         22         43          2        238          5
## SPP1                36         22         18          4         28          7
## HERC6              238        176        117        252        844        258
## NFKB1             1373       1056       1056       1288       1778       1425
## SEC24B             993        745        821        771        584        910
## EGF                151         72         61         58         14         61
## IL2                  3          0          1          2          3          0
## IL21                 0          0          1          0         15          0
## IL21-AS1             1          1          0          2          5          0
## SLC7A11             23         74         29         56        362         65
## IL15                97         62         44         70         65         69
## EDNRA              513        502        428        458        284        577
## TLR2               431        158        187         70        324        168
## FGB                  0          0          0          0          0          0
## DDX60              757        512        413        880        928        605
## SPCS3             2643       1571       2118       1818       2443       2024
## TLR3               151        157        111        151         64        161
## OSMR               900        601        514        634       1212        662
## GZMK               112         19         34         25         69         26
## GZMA               142         53         45         25        115         26
## ANKRD55              9         16          4          2          3         13
## CENPK               77         70         48         66        168         82
## CAST              8626       6636       7644       7237       5157       8338
## ERAP1             2273       1702       1675       2155       1220       2547
## ERAP2              890        141        721       1430         86        123
## TNFAIP8           1013        915        903        927        957        925
## CSF2                 3          0          1          1          6          4
## IL5                  2          3          1          1          1          2
## IL13                 2          4          1          0          1          1
## IL4                  1          1          1          1          0          3
## CD14              1410        463       1196        598        751        502
## CSNK1A1           7359       5489       5389       7232       9575       6543
## PPARGC1B           366        170        243        193        473        254
## TNIP1             3106       2204       2404       1767       3923       2397
## ATOX1              672        505        544        519        755        466
## FAXDC2            2914       1456       1909       1207        995       1499
## IL12B                6          0          0          3         52          0
## MIR146A              0          2          0          1          3          0
## PDLIM7            1171        834        698        518        435        783
## SERPINB1          1423        754       1012        850       5653        927
## SSR1              3569       2172       2175       2449       2764       2932
## CD83               228        141         98        107        401        176
## SOX4              1194       1335       1512        919        559       1301
## CMAHP              319        443        394        329        129        628
## HLA-A            21647      16232      14467      15621      12047      15284
## HLA-C            27266      12469      11826      12536      17883      22924
## HLA-B            32150      19311      21908      25826      21225      26116
## MICA               405        224        494        280        130        327
## LTA                 24         17          9          3         26         11
## TNF                 61         42         49         37         72         31
## HLA-DRB1          7657       3763       4986       6017       3758       3774
## HLA-DQB1          1715       2702       1235       1289       2479       2443
## PPARD             1538        767        829        909       2346        976
## CCND3             1599        840        793        742        961        945
## VEGFA             1265        874        456        409        983       1080
## RUNX2              100        113        134         79         65        135
## IL17A                0          0          0          0         38          2
## IL17F                1          0          0          0         49          0
## PRDM1              647        593        526        531       1942        659
## ATG5               882        621        692        638        635        623
## TRAF3IP2           958        753        797        846        941        951
## NCOA7              860        540        663        589       1369        850
## SGK1              2814       1284       1224       1064       3323       1975
## IFNGR1            2918       2130       2770       1833       4643       2231
## TNFAIP3            432        495        343        394        665        539
## SOD2              6728       4095       5730       3389      19021       5414
## LPAL2               10         10         18         13          6         11
## PLG                  4          1          2          2          1          2
## CCR6               123         88         99         93         80         94
## RAC1              6611       5342       5643       5897       5838       6698
## ZNF316            1116       1087       1174        678        560       1127
## AHR               2590       2224       2666       2696       2299       2378
## IL6                  5          4          0          2          5          1
## TOMM7             5397       4530       5419       4559       2090       3536
## CYCS              4236       1994       2461       2361       6149       2342
## AQP1             13057       9833       6911      10359       3777      11653
## NT5C3A             983        702        806        740       2465        776
## EGFR              4938       3913       4777       5124       2727       6976
## CD36              3881       2768       2351       1619       2571       1698
## SAMD9              291        254        184        263       1076        257
## SERPINE1           102         51         42         87         58        133
## CUX1              1296       1438        900       1251       1066       1765
## PSMC2             3449       1954       2309       2321       2597       2160
## NAMPT             3149       1419       2123       1877      13443       1733
## HYAL4               37         22         34          5        273         16
## LEP                296        392        444        317         36        175
## CALD1             9221       8032       6859       6972       3076       8055
## BRAF               642        668        634        572        359        749
## EZH2               415        364        302        212        527        407
## DNAJB6            4086       2553       2886       2968       4817       3106
## CSMD1               48         60         19         33         18         53
## CTSB             16890       7708       8775       6540      14259      10378
## EGR3              1952       1062        952       1080        948       1140
## TNFRSF10A          173        134        156        119        262        152
## BNIP3L            5813       3102       4387       3572       3584       3469
## DUSP4             1140        474        615        533        446        557
## NRG1               280         97        116        162        122        186
## RPL7             74332      54226      61206      53634      35146      59688
## IL7                164        162        151        215        118        195
## GEM                224        189        182        251        184        318
## MYC               1324        707        814       1037       1632       1065
## GPT               1539        625        606        550        223        508
## JAK2               806        612        642        677        621        686
## CD274               67         46         50         30        522         39
## IL33              1886       2083       1681       2033       2417       1652
## LURAP1L-AS1          4          3          0          2          1          1
## LURAP1L            434        443        322        323        229        389
## TTC39B            1961        865       1396       1215       1588        912
## IFNA1                0          0          0          0          0          0
## TEK                391        378        288        395        117        327
## TRBV20OR9-2          0          0          0          0          0          2
## TOMM5             1256        853        871        794       1154        793
## ANXA1             9098       7426       6716       7767      18430      10306
## ERP44             1162        842        884        899       1018       1004
## ZNF483             188        162        153         96         35        153
## TNFSF15             41         38         10         31         71         31
## TLR4               648        316        842        384        318        437
## PTGS1             3428       2633       3406       4885       1635       2836
## HSPA5             9427       5155       4675       6033       8960       7407
## FNBP1             1882       1499       1536       1432       1246       1683
## CARD9              142         60         61         52        115        119
## TRAF2              420        320        269        214        303        416
## CLIC3             1223        914        966        831       1002        869
## IL2RA               78         38         68         35        128         24
## GATA3             2383       3320       2602       3907        641       3808
## VIM              31721      28755      33948      25707      10191      35436
## CREM               418        243        305        286        308        272
## DKK1                32         27        232         21         21         56
## MBL2                 0          0          0          0          0          0
## SAR1A             2474       2104       1905       1897       1633       2118
## PRF1                94         34         36         35        128         53
## ZMIZ1             2324       1781       2064       1519       1674       2545
## IFIT3              524        470        485        609        953        413
## TALDO1            4814       2529       2712       2649       3456       2807
## IGF2               357        441        246        481        148        349
## INS-IGF2           334        422        225        456        138        323
## IGF2-AS              0          1          2          4          0          0
## INS                  0          0          0          0          0          0
## STIM1             2599       1653       1808       1676       1102       2303
## TRIM22             998        835        658        716       1256        740
## PTH                  0          0          0          0          0          0
## SAA1               592        427        750        222        908        233
## SLC1A2             118         63         35         70         24         85
## FOSL1               72         13         16          7        215         22
## CCND1             4992       5678       5436       7121       1756       7504
## JRKL               288        267        175        137        143        310
## MMP7              1464        319        543        252        566        806
## MMP1                20          7          0          3        353          3
## MMP3                18          6        261         13         47          9
## CASP1              936       1076        719        917       1493       1052
## DLAT              1375        485        688        789       1014        844
## IL18              2475       2347       2583       2470        738       2239
## CD3E               241        160        220        137        286        218
## MCAM              3895       2578       1956       2537       1123       2263
## WNK1              4999       3846       3796       4694       2645       4658
## TNFRSF1A          3879       2378       2103       2408       3037       2844
## GAPDH            36803      15546      15955      16468      28531      22851
## CD4               1342        689        965        738        725        936
## SLC2A3             320        233        238        285        394        276
## CLEC4D               1          3          5          1         11          0
## KLRB1              103         25         51         33         66         37
## CD69                80         37         70         37        119         31
## CLEC2B            1344       1603       1581       1728        678       1409
## OLR1                 5          0          0          1         19          0
## ABCD2               65         65         78         32         20         47
## LRRK2              373        348        417        330        159        188
## VDR               1566       1643       1079       1030       1468       1771
## TMBIM6           26438      12110      14459      12868      11479      13581
## PFDN5             8040       5575       6768       4884       3427       4578
## SP7                  2          5          1          1          0          7
## MUCL1            21938       5297       4008        349       1854       2858
## CD63             18060      11271      12071       9257       6156      12149
## SUOX              2379       1805       1813       1929       1169       2025
## RPS26            20781       2978       9469       7413       8148       7812
## RPL41            88835      61954      72154      53761      44581      53862
## IL23A               10          4          6          4         61          3
## DDIT3              376        355        330        212        164        323
## IFNG                 1          1          0          0          7          1
## IL22                 1          0          0          0          6          0
## LYZ               6647       2031       1800       2473       4999       1670
## CAPS2               87         49         65         55         14         58
## SYT1                35         30         27         40          8         37
## BTG1              5088       5311       6008       5796       3385       5200
## HCAR3              199         85        172        273        837        186
## GJB2              3748       4614       1189       1179      36058       2879
## GJB6              1785       4051        822        820      12514       2961
## TNFSF11             10          7         10          4         12          6
## TPT1            133435      91471     110628      84477      87374      78614
## LMO7              1294        906        735        767       1432       1271
## TNFSF13B           279        167         56        141        189        187
## LAMP1             7345       5132       5194       5559       3518       6352
## PSME2             1563       1040        774        941       1864       1193
## GZMB                45          9          3          4        257          6
## RPL36AL           4439       4138       3865       3139       3513       3797
## PYGL              1318       1219        955        913       1302       1404
## HIF1A             2388       1396       1221       1243       3130       1987
## FOS                616        328        298        564        206        276
## JDP2              1001        833       1307        953        316        790
## NOXRED1             29         23         24         19          6         23
## SERPINA1           182        401         49         80        490        117
## CDC42BPB          2418       1935       2075       2037       1929       2551
## PLA2G4D            387        199        277        159       9588        279
## TRIM69              14         12         14          8         29         10
## SLC51B              55         33         30         19          9         35
## SMAD3             1219       1173       1475       1070        667       1504
## CYP1A1               7         18         25        604         28        318
## AKAP13            2742       2412       2571       2797       1450       2740
## MEFV                25          9         12          9         62          6
## SOCS1              159        125         96         75        266         86
## ATXN2L            1465       1194       1124        752       1079       1404
## CD19                17         13          6          2         11          4
## ITGAL              252        158        205        109        239        170
## ITGAM              354        225        308        177        165        409
## ITGAX              188        149         89         55        286        274
## DNAJA2            2733       1731       2004       2050       2474       1951
## SIAH1              596        563        642        514        358        598
## ADCY7             1220        832        893        641        752       1159
## NOD2               438        251        267        247       1096        406
## CMTM2                5          4          6          1          6          4
## SF3B3             2819       2180       1945       2194       2695       2847
## PSMD7             3195       1918       2386       2121       2407       2110
## WWOX               274        168        145        120        223        198
## MAF               2864       4092       3242       3414       1333       4104
## SLC7A5            1545        916        827       1341       2935       1374
## CXCL16             885        591        540        626       1124        702
## XAF1               465        555        336        409        851        470
## CD68              1320        812       1784        675        846       1489
## PER1              2060       2848       1858       2672       1012       3276
## NOS2                 3         13         25         26        893         12
## TRAF4             1154        391        492        253        450        422
## CCL2               349        178        100        107        443        123
## CCL5               242        106        143        107        209        100
## CCL3                19          3          3          1        149          2
## CCR7               134         55         25         46        169         30
## STAT3             6880       3735       3784       4465      12399       5121
## SOST                83          0          0          2        162         40
## ITGA2B              15         15          9          7          6         12
## EFCAB13             64         73         94         44         29         67
## NPEPPS            1963       1583       1925       1427       2093       2041
## TBX21                9          8          4         13         11          7
## COL1A1           45240      75362       8119      66651      26498      87811
## MRPS23            1084        628        801        644        881        641
## MIR21                1          1          1          2          3          1
## RPS6KB1            899        635        751        778        721        804
## ACE                474        430        197        443        232        519
## ERN1               581        369        443        362        524        525
## PRTN3                2          0          0          0          0          0
## PLIN5             1340        333        545        267        530        278
## RETN                21          4          6          2          1          1
## CCL25                1          0          0          0          0          0
## ICAM1              699        371        480        423        716        372
## TYK2              1330        968       1068        609        805        984
## SMARCA4           2326       1799       1612       1643       1639       2255
## ACP5              1743        646        793        508        959        694
## JUNB              3634       2291       1989       1856       5163       1950
## CYP4F22           2558        728       1389       1160       2994       1083
## JAK3               217        113        110         72        301        112
## JUND              2783       1708       2588       2290        747       1863
## CEBPA             6092       4270       5220       5142       5432       4135
## CEBPG             1580       1356       1549       1597       1722       1450
## ACP7               522        240        344        255       5593        278
## ZFP36             1285       1022        829        750       1856        979
## TGFB1             1359        928       1023        793        824       1034
## RPS19            31669      23265      25432      20243      16294      20742
## PSG2                 5          0          1          0         17          3
## FUT2               111         84         66         46        395        110
## NKG7               119         25         25         20         85         32
## ZNF415             150        165        156        174         61        191
## LILRB2             207         44         99         35        183        113
## LILRA5              37          1          3          0         55          5
## KIR3DL1              0          0          2          0          0          0
## KIR3DL2              0          0          1          1          1          1
## SMOX               611        312        247        227        746        279
## BMP2               168        499        277        454        350        508
## GINS1              173        126        106        123        270        176
## PLCG1             1788       1606       1558       1033       1425       1679
## YWHAB             9444       6278       6701       7668       7254       7858
## PI3                342        120         17         30     106419        346
## MMP9               381         94         77        114        337        148
## CD40               463        387        397        329        302        401
## PFDN4              503        437        504        337        450        321
## BMP7               814        684        662       1098        582       1257
## RPS21            17925      12471      15763      10576       9364       9772
## MX1                536        332        289        508       2032        525
## PFKL              5111       3159       3291       2846       2714       4184
## IL17RA             929        676        848        644        547        641
## UBE2L3            2332       1612       1580       1703       1884       1780
## TPST2              727        495        639        485        398        509
## XBP1              8865       2163       3157       1939       4072       2917
## UQCR10            1882       1012        991        834       1157        804
## SEC14L2            516        347        278        147        290        292
## APOL6              878        707        481        560       1405        663
## APOL1              448        248        164        271       1258        311
## TYMP              2256        800        642        519       8288       1256
## BEND2                1          0          0          0          0          0
## PHEX                23         25         18         13         26         22
## TIMP1             2316       1587       1127       1202        736       1708
## FOXP3              136         46         87         63        141         85
## MSN               7047       4740       4982       5900       5782       7038
## PGK1             11197       5120       6499       5975      10558       6766
## LAMP2             5886       3950       4258       4657       3680       4723
## CD40LG              42         25         30         29         30         37
## IRAK1             2992       1473       1828       1614       2250       1993
## COX2             45451      34142      29553      31046      16921      36381
##             GSM5630002 GSM5630003 GSM5630004 GSM5630005 GSM5630006 GSM5630007
## TNFRSF9            230         16         18         21          1         17
## ENO1             25359      16143      19438      17046       9213      10302
## PIK3CD             433        134        242        151         29        226
## PGD               3054       4013       2906       3986        796       2362
## MTHFR              528        309        615        353        104        573
## TNFRSF1B          1266        379        524        395         41        482
## PINK1             1472       2190       1406       2191        509       1432
## IFNLR1             160        139        181        135         62        122
## RUNX3              986        386        369        471         38        437
## SH3BGRL3          5565       3263       3954       4054       2149       2478
## CD52               760        334        225        290        255        312
## IFI6              1632        741      20396        692        945        818
## ZC3H12A           2209        833       3854        844         55        402
## UTP11             1052        849       1103        911       1086        524
## JUN               1507        951        883       1311        236       1930
## KANK4               11         29         15         93          2        138
## EFCAB7             151        169        113        172        168        193
## IL23R                4          4          4          3          0          2
## ADGRL2             839        872        933        955        241        955
## GBP3               989        421         78         48        213        514
## GBP1              2836        524       2312        565        219        592
## GBP5               832         73        183         70         22         81
## TGFBR3            1372       1228        964       1436        632       1952
## VCAM1              834        412        272        235         58        463
## PTPN22             177         58         55         59          7         44
## CD160               18          5          7          5          3         17
## FCGR1A             114         19         68         14          9          8
## MCL1              6032       3314       4973       3905       1279       3523
## CTSK             11008      10150       8703       9642       7160      17688
## RORC               175        809        123        770        222        777
## S100A9          185832      18364     261474       4916       1151       1158
## S100A12           1038         18       1284          0          8          0
## S100A8          161703      18414     172864       4963        849       1566
## IL6R               687        392        443        422        127        340
## RIT1               770        641        730        638        454        464
## BGLAP               10          7         13         19          9          8
## IFI16             4295       1403       5924       1748        522       1664
## AIM2               153         19        150         15         17         11
## CRP                  0          0          0          0          0          0
## FCGR2A             456        169        222        156         36        186
## HSPA6              151         64        318        118         34         75
## FCGR3A             625         96        316         63         34         61
## SELL               624         81        128         44          3         62
## GLUL             17580       9974      11792       9877       1938       7071
## PTGS2               65         27         67         34         25         22
## CRB1                 6          3          4          5          0          3
## KDM5B             1563       1115       1502       1226        278       1271
## IL10                15         15         12          3         16         15
## YOD1              1458        624       4526        852        837        698
## HHAT               162        151        224        166         36        130
## TRAF5              199         81        107        103         38        250
## NLRP3               66         36         41         45          6         44
## LINC01250            0          0          0          0          0          0
## RPS7             27987      42228      23891      36201      92789      22950
## RSAD2              332         83       2013         88         41        115
## FOSL2             3136       2179       3889       2747        257       3180
## REL               1138        593       1136        590        191        648
## TGFA              1866       1052       1264       1102        417        615
## DYSF               345        171        211        210         15        238
## HK2               2099       1063       1997       1116         73        883
## CD8A              1103        205        218        141         62        127
## CD8B               410         99         64         69         54        108
## EIF5B             3482       2515       2335       2697        780       2446
## IL1R1             2106       1436       1503       1632        343       1645
## RGPD6              236        219        173        245         84        362
## IL1A                57        164         38         85          3         38
## IL1B                77         56         34         55          0          7
## IL37               298       1009        669        870        627        601
## IL36RN            7306        809      10911       1134       2884        918
## IL1F10              88        108         98         94         89         65
## IL1RN             2569       1148       1990       1404        429        754
## NMI                956        543       1429        567        702        440
## TNFAIP6            159         55         74        111        156        292
## IFIH1              683        272       1847        320         75        397
## SCN1A                1          2         19         10          4         10
## ABCB11              16         49          5         35          1         47
## RBM45              179         99        132        141         55        128
## FRZB               503        459        458        635        152        543
## TFPI               684        639        460        636        244        667
## STAT1             8183       1634       9468       1578        530       1753
## NABP1              335        140        372        161         39        257
## SF3B1             4896       3618       3680       3697       1405       4909
## CASP10             378        173        452        196         95        252
## CD28               286         49         96         51          9         72
## CTLA4              211          9         21         11          1         16
## ICOS               244         15         26         15          0         18
## NDUFS1            2229       3244       2349       3084       1376       1974
## CXCR2              317        131        398        117         15         69
## IRS1               194        298        274        507         42        610
## CCL20               57         11         54         19          1          9
## ATG16L1            453        445        393        486        225        458
## GPR35               21          7         22         12          0         20
## PDCD1               66         12         18         12          0          6
## PPARG              217       1110        311        955         43        656
## RPL15            41230      56761      35668      55263      72025      33322
## EOMES               82         12         25          9          1         13
## CX3CR1             153        151        127        135          9        101
## ACKR2              185         20        308         19         16         40
## CCR2               302        247        212        233         23        193
## CCRL2               34         17         26         17         13         11
## TLR9                20          5          6          6          1          6
## ARHGEF3           1078        580       1196        658        415        577
## ADAMTS9            132         75         51        137          7        185
## TMEM45A          16532      19942      18843      18662      13087      10053
## CD80                26          6          0          7          2          7
## CD86               347        167        137        176         57        127
## MIX23              284        231        246        273        503        219
## PLS1               150         65        133        135         36        114
## PTX3                28         23         28         21          4         25
## GOLIM4             993        574        701        913        316       1168
## MYNN               633        614        635        707        951        545
## TNFSF10           3219       1841       4202       2013       2263       1677
## ADIPOQ            1198          8        871       1235          9       1709
## SPON2              688        261        721        540        242        864
## S100P             1002        516        510        460        249        226
## WDR1              7641       5193       7038       5616       1628       4102
## CD38                42          5         28          5          0         20
## PPARGC1A           164        505        101        386         14        338
## TMPRSS11B            1          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          2          0          1          0          7
## CXCL8             1094          5         84          2         21          1
## CXCL2               38          1         27          3          4          7
## AREG               152        154         50        165         67         75
## CXCL10             921         93       1049          9         26         64
## CXCL13             833         54         52         24          0         11
## SPP1                86         71        101         18          1         21
## HERC6              564        138       3147        144         59        166
## NFKB1             1677        707       1590        928        143       1019
## SEC24B             676        606        699        695        350        732
## EGF                 18         42         10         53          6         66
## IL2                  2          1          4          0          0          3
## IL21                24          0          2          0          0          1
## IL21-AS1             9          1          1          0          0          1
## SLC7A11            174         20        227         37         75         50
## IL15               154         94         58         77         48         90
## EDNRA              498        192        500        335         40        279
## TLR2               188        306        248        245         51        173
## FGB                  0          0          0          0          0          0
## DDX60              888        334       2363        440        137        523
## SPCS3             2930       2446       2584       2949       2138       1730
## TLR3               191         69        172        100         43         97
## OSMR               791        336        736        444         76        492
## GZMK               333         63         62         35          3         66
## GZMA               349         86        149         53         35         60
## ANKRD55             17          8          3          2          4         11
## CENPK              158        117        164        121        295         71
## CAST              8393       6969       7516       7506       2464       5531
## ERAP1             2205       1567       1623       1498        369       1442
## ERAP2             1368        625        946        522        173        640
## TNFAIP8           1417        906       1191       1032        997        849
## CSF2                10          8          3          2          0          5
## IL5                  0          0          0          3          0          1
## IL13                 5          0          4          2          0          0
## IL4                  0          0          0          0          2          2
## CD14              1198        692        901        810        344        791
## CSNK1A1          10737       6365      13457       7462       4094       5161
## PPARGC1B           296        198        222        224          8        250
## TNIP1             4366       2348       3403       2660        433       1962
## ATOX1              737        694       1003        670       1108        480
## FAXDC2            1047       2084        754       3136         78       1913
## IL12B               16          1          4          1          0          1
## MIR146A              3          1          1          3          0          1
## PDLIM7             595        476        557        440         91        719
## SERPINB1          3281       1055       1448       1063       1066        976
## SSR1              3339       2603       2457       2972       1024       2220
## CD83               596        137        189        180         39        161
## SOX4               957        656        660        835        204        987
## CMAHP              164        266        107        261        232        346
## HLA-A            33579      17569      21899      12262       4895      11303
## HLA-C            26644      13475      18695      11757       9006      13821
## HLA-B            49803      23702      33837      21639       5487      16587
## MICA               264        299        312        322        422        288
## LTA                 29         10         13         12          0         11
## TNF                 81         32         60         46          9         32
## HLA-DRB1          8692       4993       5016       5318       2243       5442
## HLA-DQB1          6802       3834       2873       2803        822       2674
## PPARD             1853        813       2912        983        127        793
## CCND3             1438       1015       1102       1191        256        850
## VEGFA              805        668        505        621         75        613
## RUNX2              132         54         67         42         13         87
## IL17A               17          2          3          1          0          0
## IL17F               10          0         13          1          0          0
## PRDM1             1341        387       1748        613        280        396
## ATG5               851        844        749        898        840        693
## TRAF3IP2          1056        740       1285        916        187        645
## NCOA7             1120        518       1067        855        198        738
## SGK1              3413       1387       3558       1737        837       1628
## IFNGR1            3690       3216       3903       2890       2415       2866
## TNFAIP3            750        285        440        381         56        521
## SOD2              9537       5849       8132       5163       1314       3933
## LPAL2                6          5          5          7          2         12
## PLG                  2          5          1          1          0          1
## CCR6               151        122         47        112          8        118
## RAC1              7694       5452       7147       6229       3045       4453
## ZNF316             556        336        417        457         29        765
## AHR               2528       1820       3191       2632       1023       2672
## IL6                  3          2          2          4          2          3
## TOMM7             4200       5859       3647       5548       3876       3427
## CYCS              5393       4586       4873       4213       4639       2513
## AQP1              8614       5630       7785       8782       7615       7282
## NT5C3A            2405       1111       3878       1106        916        616
## EGFR              2538       1906       2060       2344        386       4016
## CD36              6121       3514       9244       5034       2727       4291
## SAMD9             1179        181       2031        163         26        185
## SERPINE1           249         65        215        142        246        159
## CUX1              1230        696       1408        939        152        867
## PSMC2             3524       3200       3165       3238       2917       2250
## NAMPT             6259       3532       6829       2938       1378       2189
## HYAL4              105         38        280         14          9         27
## LEP                504          3        181        220          2        622
## CALD1             5372       5717       3829       4967        641       6091
## BRAF               442        366        379        405         95        539
## EZH2               501        238        588        318        244        237
## DNAJB6            5867       4424       8578       4526       2601       3070
## CSMD1               12         40          2         34          7         42
## CTSB             19174      12517      18909      14082       2972       8228
## EGR3               690       1230        977       1696        288       1113
## TNFRSF10A          215        117        212        130         97        131
## BNIP3L            5016       7297       6584       6134       3546       3893
## DUSP4              766        628        390        804         63        821
## NRG1               103         43        108        143         18        102
## RPL7             61235      85815      41034      77863      64301      45802
## IL7                119        117        188        167        108        206
## GEM                408        176        288        209         57        256
## MYC               1174        758       1394        969        253        801
## GPT                226       1638        134       1652         24        716
## JAK2               806        531        740        536        218        665
## CD274              239         30        166         24          3         27
## IL33              1685       1997       1746       1374        504       2233
## LURAP1L-AS1          2          2          4          3          3         10
## LURAP1L            447        393        492        385        252        351
## TTC39B            1254       3138       1768       2653       1108       1452
## IFNA1                0          0          0          0          0          0
## TEK                294        149        202        191         33        261
## TRBV20OR9-2          0          0          0          0          0          3
## TOMM5             1280       1416       1346       1402       2327        952
## ANXA1            15623       7287       5565       8887       9721       7883
## ERP44             1359       1120       1095       1084        828        896
## ZNF483              80         85         38         79         37        119
## TNFSF15             24         27         28         20          0         20
## TLR4               591        408        401        439        254        563
## PTGS1             2740       1339       2709       2436       1579       2408
## HSPA5             9140       7687       6576       7446       3219       6114
## FNBP1             1935        984       1260       1008        362       1275
## CARD9              101         62         79         54         18         98
## TRAF2              381        272        310        358         34        261
## CLIC3             1146        795       2295       1140       1056        596
## IL2RA              260         36         33         13          2         41
## GATA3             1068       1528       1095       2160        676       1888
## VIM              33881      17963      24638      29883       9564      28266
## CREM               422        418        337        370        355        361
## DKK1                38         39         10         37          4         57
## MBL2                 3          0          0          0          0          0
## SAR1A             2276       2029       1955       2139       1961       2053
## PRF1               316         56         85         39          8         52
## ZMIZ1             1608        932       1152       1204        156       1785
## IFIT3             1374        446       4496        396        299        606
## TALDO1            4313       6772       4065       5338       3042       3098
## IGF2               245        137        230        180         26        309
## INS-IGF2           232        132        207        175         26        286
## IGF2-AS              1          0          0          0          0          2
## INS                  0          0          0          0          0          0
## STIM1             1710       1021       1580       1467        248       1539
## TRIM22            1947        763       3736        778        209       1120
## PTH                  0          0          0          0          0          0
## SAA1               361       1621        427       1011         13        648
## SLC1A2              49         17          5         42         14         49
## FOSL1              118         17        130         51         10         17
## CCND1             2666       2373       1139       3124        404       3832
## JRKL               139         91        105        122         24        156
## MMP7               382        862        314        295        534        214
## MMP1               265         19        355         12          0         17
## MMP3                86         12         40          1          6          6
## CASP1             1563        873       1717       1111        928        820
## DLAT               907       1048        970       1033        327        683
## IL18              2644       2979       2720       3242       4841       1726
## CD3E               933        214        211        184          8        191
## MCAM              2351       2291       2446       2400        350       2693
## WNK1              3116       2073       2707       2881        328       3643
## TNFRSF1A          3309       2393       3775       3246        741       2200
## GAPDH            43615      25767      39847      27820      16164      17886
## CD4               1476        602        799        675         70        819
## SLC2A3             538        202        273        293         55        223
## CLEC4D              12          3          2          1          0          2
## KLRB1              112         64         68         65          4         38
## CD69               197         99         64         63         32         93
## CLEC2B            1503       1216       1762       1411       6420       1363
## OLR1                 9          6          3          1          0          6
## ABCD2              104         19         55         38          1         50
## LRRK2              289        206        299        228         65        427
## VDR                932        726        742       1105         93        890
## TMBIM6           13965      25043      12239      23803       4169      14114
## PFDN5             6923       9358       5232       8343      22142       6591
## SP7                  5          0          0          0          0          2
## MUCL1             4611        963       2926       4752       1276       7520
## CD63             13672      12219       9775      14578      20649      14103
## SUOX              1648       2122       1462       2186        336       1607
## RPS26             5521       6811      10485      14391      23343       8617
## RPL41            73800     112705      59225     102306     170784      61802
## IL23A               16          3         26          7          0          3
## DDIT3              246        261        241        251        398        312
## IFNG                26          2          2          0          2          3
## IL22                 3          1          1          2          0          0
## LYZ               8241       2841       4693       2553       1644       5479
## CAPS2               27         66         40         46         36         81
## SYT1                24         15         14         21          6         30
## BTG1              7202       6270       8441       5609       3638       4648
## HCAR3              425        149        306        140         57        179
## GJB2             22747       6326      34017       4358        965       1470
## GJB6              8023       3378      12124       2579       2796        853
## TNFSF11             29         32         15         23          1         17
## TPT1            134368     163998     112632     152793     308781      99656
## LMO7              1238        448       1481        692        207        737
## TNFSF13B           413        213        204        150        113        233
## LAMP1             4684       4067       4596       4753        576       4283
## PSME2             2866       1405       2245       1475       1588       1053
## GZMB               361         13         77         17          3         24
## RPL36AL           4603       4839       3879       5332       6574       3729
## PYGL              2166       1063       2425       1095        362        843
## HIF1A             2616       1172       2167       1316        364       1112
## FOS                462        616        233        546        490        645
## JDP2               763        525        806        894        390        996
## NOXRED1              8         10         15         12          2         17
## SERPINA1           407        146        392        178          2        134
## CDC42BPB          1966       1024       1771       1398        100       2022
## PLA2G4D           3761        482       7235        334        215        263
## TRIM69              42          7         22         22         11         21
## SLC51B              32         30         15         36         10         50
## SMAD3              874        718        763        580        150        984
## CYP1A1               6         30          1        192         22        223
## AKAP13            2123       1070       1070       1429        140       2351
## MEFV                73          2         26          3          0         10
## SOCS1              157         92        125        102         36        110
## ATXN2L             963        480        912        658         64       1074
## CD19                13          9          2          4          0          4
## ITGAL              561         95        148         66          2        176
## ITGAM              275        127        153        147         77        253
## ITGAX              147         48         76         69          4        193
## DNAJA2            2803       2533       3147       2682       2580       1875
## SIAH1              504        494        595        523        394        540
## ADCY7              823        335        710        443        100        991
## NOD2               680        298       1063        342         81        263
## CMTM2                3          6          2          1          0          5
## SF3B3             2497       2247       2557       2408        334       1831
## PSMD7             3056       3541       2960       3422       2891       2089
## WWOX               264        205        655        184        124        148
## MAF               3010       1983       3529       1997       1310       2605
## SLC7A5            1641        906       2666       1344         58        799
## CXCL16            1051        598        780        814         90        507
## XAF1               638        171       2630        213         57        540
## CD68              1875        677       1471       1001        372        725
## PER1              1913       1476       1040       1366        609       3142
## NOS2               184          1         15          1          3          5
## TRAF4              539        788        665        729        456        439
## CCL2               435        276        492        267         98        187
## CCL5               940        221        287        162         25        167
## CCL3                48          4         15          3          3          9
## CCR7               546         45         67         42          1         54
## STAT3             9586       3678       7312       4479        443       3892
## SOST                42          2         26          0          2         50
## ITGA2B               8         16         12         10          4          7
## EFCAB13             43         30         21         46         27         71
## NPEPPS            1965       1421       2044       1575        562       1610
## TBX21               41          8          9          3          0          6
## COL1A1           41821      16336      53945      11933       1384      81342
## MRPS23            1082       1093        998       1076       2374        774
## MIR21                1          0          1          1          0          2
## RPS6KB1            869        565        873        711        186        616
## ACE                449         93        457        192         23        581
## ERN1               415        189        398        250         38        374
## PRTN3                0          0          0          0          2          0
## PLIN5              238       1135        212       1053          0        744
## RETN                 6          3          6          4          0          2
## CCL25                2          1          0          1          0          0
## ICAM1              713        294        411        271         67        369
## TYK2               742        362        741        561         49       1107
## SMARCA4           1542        889       1423       1212        109       1436
## ACP5              1890       1386       1844       1460        632        814
## JUNB              3374       2369       4450       2717       1167       1500
## CYP4F22           2362       2747       2886       2452        271       1550
## JAK3               322         56         83         55          1        138
## JUND              1623       1450       1794       2435        484       2326
## CEBPA             4449       5494       7163       6556       2218       4306
## CEBPG             1734       1512       2140       1823       1150       1338
## ACP7              2262        478       3879        348         89        269
## ZFP36             1154        538       1123        716        131        760
## TGFB1             1547        628       1290        945        102        756
## RPS19            31069      39151      29746      36693      53456      23963
## PSG2                 6          0          0          0          0          0
## FUT2               354         73        348         96         83         48
## NKG7               293         44        116         32         17         61
## ZNF415             120        152         86        239        112        205
## LILRB2             185         44         83         58         21         65
## LILRA5              31          3          7          3         13          6
## KIR3DL1              0          2          0          0          0          0
## KIR3DL2              2          0          0          0          0          1
## SMOX               574        459       2009        532        154        221
## BMP2               388        217        182        346        196        342
## GINS1              286        198        283        185        304        120
## PLCG1             1321        640       1464        728        107       1164
## YWHAB             9901       7753       7842       8964       2964       6121
## PI3              35504        436      21874        197         14         66
## MMP9               836        118        476         48          1        180
## CD40               535        335        475        351        140        276
## PFDN4              525        589        380        538       1142        433
## BMP7               623        488        916        839        196        522
## RPS21            16181      23969      13612      20323      63640      13935
## MX1               1282        272       6384        279         27        332
## PFKL              2967       2993       2858       3449        287       2882
## IL17RA             754        490        655        610         62        572
## UBE2L3            2717       2516       2402       2585       1703       1580
## TPST2              718        501        802        558        173        621
## XBP1              4165       5352       4381       5699       2125       4642
## UQCR10            1485       2604       1344       1978       1383       1093
## SEC14L2            761        627        392        480        141        328
## APOL6             2007        398       2328        526        105        684
## APOL1             1537        219       1155        178         47        218
## TYMP              6919       1866       9099       1880        243        981
## BEND2                0          1          0          0          0          0
## PHEX                63         20         46         22         20         30
## TIMP1             1647       1239       1606       1293        462       1379
## FOXP3              371         54         68         64          6         63
## MSN               9232       3987       7045       5098       1298       4639
## PGK1             13261      11692      11805      10631      13761       6923
## LAMP2             4788       5219       4183       5063       2857       3800
## CD40LG              58         20         39         19          1         18
## IRAK1             2591       1628       2757       2075        578       1890
## COX2             22027      24262      11948      30015       5172      32235
##             GSM5630008 GSM5630009 GSM5630010 GSM5630011 GSM5630012 GSM5630013
## TNFRSF9             42          3         14         49         96         15
## ENO1             24603      10657      26507      23486      19444      19681
## PIK3CD             602        263        293        330        538        409
## PGD               3216        996       2332       5330       3495       3141
## MTHFR             1653        676        456        576        987        798
## TNFRSF1B          1771        780        754       1045       1499       1097
## PINK1             2533       1974       2039       2617       1555       1786
## IFNLR1             419        210        196        161        306        297
## RUNX3             1729        661       1140        912        939       1740
## SH3BGRL3          4440       2940       4764       4682       4219       2773
## CD52               205        147        451        328        441        217
## IFI6              9931       1033       1326       1283       4883        875
## ZC3H12A           4628        420        692       1281       4524        584
## UTP11             1062        705       1036        764        918        693
## JUN               2604       1744       1690       1627       1247       1984
## KANK4                8          8         28        117         12        165
## EFCAB7             206        178        183        135        156        158
## IL23R                2          1          2          3          8          0
## ADGRL2             883        627        787       1030        610        807
## GBP3               476        187        447        309        721        563
## GBP1              1158        341        794        746       1229        868
## GBP5               442        109         81        139        346        160
## TGFBR3            6001       5285       2095       2117       1330       2762
## VCAM1              381        463        529        740        432        415
## PTPN22              93         44         69         82        105         54
## CD160               11          8          7          6          9         13
## FCGR1A              28          8         19         15         23          6
## MCL1              8276       5041       6012       5259       5777       4246
## CTSK             17967      31136      13559      16179       5013       6178
## RORC               449        604        604        954        181        827
## S100A9           90612        195      24021      16684     180837       2188
## S100A12            222          2         36          4        684          2
## S100A8           50725         70      20578      15384     182911       3636
## IL6R              1208        780        571        667        772        604
## RIT1              1050        589        777        727        764        515
## BGLAP               13         10         11         10          9         18
## IFI16             6316       1727       3057       2414       5352       2599
## AIM2                15         12          7         16         42          2
## CRP                  1          0          0          0          0          0
## FCGR2A             298        242        165        100        146         78
## HSPA6              300        136        127         84        268         75
## FCGR3A             200         53         68         55        110         40
## SELL                86         38        184        174        255         82
## GLUL             37482      29717      11689      13840      10788       7016
## PTGS2               68         34         76         23         51         23
## CRB1                 3          6         12         10          3          2
## KDM5B             3746       1421       1527       2046       2255       1604
## IL10                 7          2          4          8          8          0
## YOD1              2941       1066        737        524        853        371
## HHAT                70         49        200        184        164        233
## TRAF5              299        276        206        171        310        259
## NLRP3               81         62         39         50         67         44
## LINC01250            0          0          2          3          0          0
## RPS7             22343      24347      32630      25630      23370      22586
## RSAD2              361        113        219        149        133         90
## FOSL2            11578       4575       4010       4887       4513       4826
## REL               3898        987        987        931       2181       1240
## TGFA              1661        709        779        927        609        356
## DYSF               415        231        361        376        386        509
## HK2               1994        420        735       1634       1161        873
## CD8A               326        151        165        166        256         75
## CD8B               109         64        126         76         88         27
## EIF5B             6744       3643       4060       3959       4663       5153
## IL1R1             4109       2307       2365       2152       1949       2159
## RGPD6              808        615        333        323        366        544
## IL1A                 7         40         31         55          6         13
## IL1B                20          4         27         71         25          7
## IL37               687       1130        559        415        141        107
## IL36RN            5320       1404       2328       1018       5504        168
## IL1F10             273        218        109         54         62         14
## IL1RN             3542       1166       2249       2046       2318        932
## NMI                822        361        842        602        796        401
## TNFAIP6             81        247        148        115         98         51
## IFIH1             1181        289        618        448        814        483
## SCN1A                5          5         19          6          6          6
## ABCB11               9         10         14         67         31         52
## RBM45              219        149        227        140        202        203
## FRZB               612        260       1487        648        594       1654
## TFPI              1219       1249        739        805        491        540
## STAT1             9214       1948       3439       3163       6024       2938
## NABP1              154         97        228        180        311        223
## SF3B1             9661       6746       5021       4782       6632       6477
## CASP10             466        250        310        301        542        372
## CD28               146         24         86        111        192         56
## CTLA4               53          7         37         23        140         27
## ICOS                79         10         34         37        119         27
## NDUFS1            3295       2030       2541       3066       2168       2427
## CXCR2              266         45        125        198        455         73
## IRS1               613        448        402        647        293        672
## CCL20              145          0         76         77        121          2
## ATG16L1           1162        726        753        658        680        679
## GPR35               49         38         14         33         46         30
## PDCD1               52         16         18         34         57         17
## PPARG              161        153        181        779        101        431
## RPL15            31233      35905      50369      44002      34874      32851
## EOMES               88         33         17         34         45         17
## CX3CR1             228         82        161        232        198        134
## ACKR2               65         27         46         26        166         23
## CCR2               224         82        396        303        200        115
## CCRL2               18         17         32         49         14         18
## TLR9                17          3          5          7         19          7
## ARHGEF3           1451        796       1163        935       1040        674
## ADAMTS9            100         47        223        128        113        288
## TMEM45A          17184       7782       8554      16363      15071       3556
## CD80                 4          0          5          7         19          3
## CD86               203        183        229        142        192         81
## MIX23              234        181        286        189        245        232
## PLS1               189         90        157         90        149        177
## PTX3                95         96         72         48         24         62
## GOLIM4            1442       1328       1355       1109        945       1504
## MYNN               705        616        682        619        522        498
## TNFSF10           4241       1527       3740       2247       3983       2359
## ADIPOQ              49         47        511        104         97        638
## SPON2              752       1036        931        785        847        968
## S100P              957        382        840        327        206       1194
## WDR1              7939       4665       7057       6378       6933       6013
## CD38                12         36         11         13         37         17
## PPARGC1A           215        183        452        333         88       1469
## TMPRSS11B            0          0          0          0          3          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          3          3          1          2          9
## CXCL8               14          1          1          1         63          2
## CXCL2               15         10          7          3         31          9
## AREG                85         24        200        136         99         97
## CXCL10             231         20         25         57        153        110
## CXCL13              76          0          2        127        100         13
## SPP1                 6         19          8         77         88        158
## HERC6             3064        169        410        279        926        373
## NFKB1             3047       1248       1627       1618       2038       1417
## SEC24B            1600        971        821        861       1024       1025
## EGF                 12         13         71         39         15        108
## IL2                  0          0          3          1          1          0
## IL21                 1          0          0          1          7          0
## IL21-AS1             0          0          0          4          2          1
## SLC7A11            238         25         43         45        262         27
## IL15               114        100         66         74        142        146
## EDNRA              402        250        594        417        489        583
## TLR2               415        176        158        386        240        175
## FGB                  0          0          0          0          0          0
## DDX60             1938        482        721        621       1123        431
## SPCS3             3074       2490       2655       2478       2399       1903
## TLR3               296        142        212        189        202        159
## OSMR              1785        761        810        853       1019        695
## GZMK               106         44         54         87         61         25
## GZMA               119         46        122         79         95         53
## ANKRD55             11          9         20         10         22          7
## CENPK               49         24        126         68        154         91
## CAST             16588       9858      10113       8751       6422       7914
## ERAP1             4214       1935       2794       2448       2095       2448
## ERAP2              203         88        108         95       2737       2142
## TNFAIP8           2070       1122       1184       1234       1393        836
## CSF2                 1          0          3          5          4          0
## IL5                  0          2          1          2          1          6
## IL13                 4          0         14          0          0          1
## IL4                  1          0          0          1          0          1
## CD14              1160       1332        838        735        621        385
## CSNK1A1          13457       6325       9417       7372      10302       5621
## PPARGC1B          1098        215        228        425        717        301
## TNIP1             5472       2426       3271       3362       3121       2381
## ATOX1              809        460        728        533        820        446
## FAXDC2            2491       1830        942       3396       1128       1362
## IL12B                0          0          0          4         13          1
## MIR146A              3          1          1          1          9          1
## PDLIM7             737        785        928        527        912       1159
## SERPINB1          1325       1146       1697       1188       1262       1064
## SSR1              3715       2698       3306       3344       5029       4737
## CD83               241         43        324        412        523        288
## SOX4              1657       1509       1244       1299       1330       2669
## CMAHP              299        331        485        335        155        410
## HLA-A            44862      21463      25485      24201      30997      28521
## HLA-C            42326      20340      30776      32128      27761      23932
## HLA-B            62519      28264      34087      33947      39711      33033
## MICA               386        315        343        247        404        390
## LTA                 25         12         21         17         18         25
## TNF                 76         29         92         77        108         46
## HLA-DRB1          6781       4368      11731      10914       3354       2278
## HLA-DQB1           656        438       5184       5171        882        587
## PPARD             3843        876       1153       1481       1929        889
## CCND3             2519       1440       1267       1385       1201       1015
## VEGFA              812        497       1014        949        657       1296
## RUNX2              201        150         90        102         98        134
## IL17A                5          0          0          1         22          0
## IL17F                1          0          1          1         26          0
## PRDM1             2462        575        497        656       1166        223
## ATG5               854        814        971        783        777        671
## TRAF3IP2          1737        860       1193       1108       1300       1027
## NCOA7             1684        974        873        878       1168        749
## SGK1              4214       1042       3039       1609       3658       2839
## IFNGR1            4213       3538       3394       3007       3353       2511
## TNFAIP3            927        291        582        659        809        550
## SOD2              9888       5608       7769       7568       7439       5832
## LPAL2                8          4          6          6         16         12
## PLG                  1          2          1          3          0          1
## CCR6               165         54        160        156        130         88
## RAC1             11692       6961       8704       8121       9539       6780
## ZNF316            1718       1018        732        735       1399       1610
## AHR               3398       1934       2912       2698       2994       2358
## IL6                  3          1          7          2          4          7
## TOMM7             3016       4233       3920       3577       4201       4728
## CYCS              3218       1580       4088       3654       3544       2662
## AQP1             14840      14149      17430      16157      10196      16347
## NT5C3A            2449        910        923        878       1549        482
## EGFR             12766       6152       4354       4817       4578       7215
## CD36              1960        943       1449       4175       3574       1929
## SAMD9              983        166        250        244        640        222
## SERPINE1           485        233        154         72        177         86
## CUX1              2258       1149       1678       1327       1530       1459
## PSMC2             4356       2866       3413       3265       2973       1998
## NAMPT             5897       2502       3094       3002       3877       2533
## HYAL4              118          7         54         33        178        119
## LEP                 35         16        138         25         63        246
## CALD1             9070       9366       9526       6526       4952       7583
## BRAF              1161        661        532        542        620        658
## EZH2               949        313        418        351       1018        489
## DNAJB6            5793       3343       4937       4245       4573       2493
## CSMD1                5         26         58         44         15         38
## CTSB             15544      10628      16179      19230      12912       9225
## EGR3              1859        580        747       1779        706        567
## TNFRSF10A          349        166        170        137        193        170
## BNIP3L            8822       5237       4080       5994       3152       2466
## DUSP4              472        340        419        922        490        994
## NRG1               191         61        171        134        103        257
## RPL7             58290      62451      83852      71876      47545      47803
## IL7                181        131        154        150        180         77
## GEM                311        139        458        231        439        233
## MYC               2937       1006       1400       1253       1838        918
## GPT                182        124        205       1935        335        461
## JAK2              1779       1186        830        831        934        621
## CD274              151         38         66         63        168         57
## IL33               922        834       2513       1971       1668       1538
## LURAP1L-AS1          7          6          1          3          3          0
## LURAP1L            496        281       1095        429        477        555
## TTC39B            1693        665        817       2306       1405       1012
## IFNA1                0          0          0          0          0          0
## TEK                378        219        386        388        230        390
## TRBV20OR9-2          2          0          0          0          0          0
## TOMM5             1064        864       1172       1065        983        745
## ANXA1             7563       8175       8970       6531       4038       6419
## ERP44             1621       1198       1260       1150       1256        947
## ZNF483             163        194         77         77         95        147
## TNFSF15             26          7         38         58         36         63
## TLR4              1168       1631        520        397        207        227
## PTGS1             9252       4907       3767       3416       3681       2526
## HSPA5            11463       5816       8914      11397       8407       8102
## FNBP1             3198       1852       1650       1486       2267       1608
## CARD9              144         53        139        119        204         92
## TRAF2              527        199        470        478        629        513
## CLIC3              930        737        816        930       1940        454
## IL2RA              142         46         48         42        131         49
## GATA3             5013       2567       2770       3282       2653       3820
## VIM              44629      52531      36161      34352      23275      31418
## CREM               385        348        447        375        292        308
## DKK1               477        746         68         24         15         83
## MBL2                 0          0          0          0          3          0
## SAR1A             2633       2447       2526       2336       2175       2351
## PRF1               154         68         65         62         88         51
## ZMIZ1             4546       2184       1683       2028       2309       2711
## IFIT3             1988        576        986        710       1276        636
## TALDO1            3255       1824       3365       4935       3987       2855
## IGF2               442        285        447        465        557        823
## INS-IGF2           424        260        416        432        502        764
## IGF2-AS              2          3          1          0          2          4
## INS                  1          0          0          0          0          1
## STIM1             3430       2203       2749       2056       1515       2427
## TRIM22            2515        857       1136        886       1688        871
## PTH                  0          0          0          0          0          0
## SAA1               222         20         64        816        184       1319
## SLC1A2              24         40         31         73         53         59
## FOSL1              138         21        240         23         68         14
## CCND1             3935       3073       4002       5262       4385       7342
## JRKL               266        144        241        221        203        311
## MMP7               293        306        872        295        206       1739
## MMP1                 0          3         28        126         52         14
## MMP3               737        796         25         19          2         39
## CASP1              873        438       1332        846       1509        829
## DLAT              1397        792       1042       1186        798        853
## IL18              2650       1830       2753       2038       2162       1234
## CD3E               363         87        279        385        514        147
## MCAM              3942       2301       3533       3301       2844       4568
## WNK1             14544       6925       4165       5345       4269       4215
## TNFRSF1A          5769       2800       4193       4080       4257       3074
## GAPDH            36975      21142      45621      30895      36523      37010
## CD4               1460       1197       1346       1249       1260        678
## SLC2A3             604        376        354        378        361        409
## CLEC4D               4          0          1          0          3          0
## KLRB1              111         32         70         74        124         40
## CD69                79         82         91         60         79         44
## CLEC2B            2290       2169       2535       1425       2558       1759
## OLR1                 3          0          1         10          3          1
## ABCD2               33         39         61         29         29         41
## LRRK2              465        328        230        224        292        264
## VDR               1922        728       1042       1681       1388       1593
## TMBIM6           15703      11145      15825      26047      10567      13729
## PFDN5             5090       6115       8176       6156       5424       6974
## SP7                  1          2          0          0          2          7
## MUCL1             3160         57      13093        585       1544      11171
## CD63              9913      15661      17474      15235       9133      11394
## SUOX              2459       1769       2072       2607       1804       1891
## RPS26             8467       8071      11817      10976       4853       3795
## RPL41            48701      63320      87854      76925      62312      58712
## IL23A               26          9         10         11         24          8
## DDIT3              495        436        361        259        318        501
## IFNG                 3          1          3          1         12          8
## IL22                 0          0          1          0          3          1
## LYZ               3519       1259       6494       5402       8949       1358
## CAPS2               41         77         55         59         30        101
## SYT1                14         62         27         30          9         38
## BTG1             13303       7551       8256       7622       8856       6644
## HCAR3              484        126        322        296        626        174
## GJB2              7454        670       6227       7392      16776       4027
## GJB6              4210        671       3764       2647       5662       2906
## TNFSF11              8          5         10         12         13         11
## TPT1            107918     110121     155897     118691     106412      79430
## LMO7              2244        651       1427        873       1323        747
## TNFSF13B           146        109        220        265        323        193
## LAMP1            11336       7239       6031       8660       6160       7271
## PSME2             1915        853       2142       1605       2097       1563
## GZMB                65         19         52         36        127         10
## RPL36AL           3949       3547       5738       4277       4084       3339
## PYGL              2059        869       1789       1152       1996       1225
## HIF1A             3001       1482       2558       1588       2058       2928
## FOS                616        396        764        420        255        301
## JDP2              1289       1199       1095        875        843        728
## NOXRED1             50         24         19         13         14         17
## SERPINA1           194         53        158        210        218         90
## CDC42BPB          4540       2167       2349       2377       2627       2482
## PLA2G4D           3002        208        541        612       3557         89
## TRIM69              26          6         17         12         22         14
## SLC51B              44         50         40         37         11         41
## SMAD3             3022       1348       1139       1162       1526       1366
## CYP1A1             140         46         54         24         19          8
## AKAP13            5721       3266       2217       2317       2341       2839
## MEFV                37         22         12         19         23         12
## SOCS1              149        167        112        123        175        145
## ATXN2L            2061       1077        966       1056       1737       1471
## CD19                 8          0          2          8         15         13
## ITGAL              348         96        194        212        552        214
## ITGAM              278        381        265        205        230        162
## ITGAX               61         52        131         78        254        213
## DNAJA2            3684       2546       2872       2415       2394       1770
## SIAH1              776        633        605        483        666        750
## ADCY7             1114        882        752        743       1192        745
## NOD2              1439        260        411        351       1144        284
## CMTM2                1          1          0         15         11          5
## SF3B3             3540       1843       2824       3209       3157       2193
## PSMD7             4614       2812       3060       3364       2915       2348
## WWOX              1405        329        203        240        263        224
## MAF               6519       4198       3750       3277       4723       3940
## SLC7A5            5074        674        640       1772       4091       2232
## CXCL16            1070        553        835        954       1037        789
## XAF1              2627        373        432        298       1559        679
## CD68              1448       1829        980        861        770        374
## PER1              5181       4219       2553       2063       1554       2771
## NOS2                30          8         15         15         92          8
## TRAF4              670        304        835        575        656        948
## CCL2               129         47        561        386        458        306
## CCL5               530        192        231        319        236        104
## CCL3                17          9          2         10         21          4
## CCR7               153         17        161        403        367        138
## STAT3            11469       3969       7473       7098       8628       6877
## SOST                 0          0        348          5         12         14
## ITGA2B               6         10         15          4         11         17
## EFCAB13             57         64         34         39         48         73
## NPEPPS            2421       1490       1871       1756       2159       1606
## TBX21               25         10         16         17         21         13
## COL1A1           31919      16479      72813     106105      57213      90373
## MRPS23            1094       1022       1058        834        877        781
## MIR21                2          0          1          1          1          1
## RPS6KB1           1848       1182        903        877        915        865
## ACE                455        291        493        487        710        950
## ERN1              1056        491        504        503        652        569
## PRTN3                0          0          0          1          0          4
## PLIN5              383         20         52       1263        493        465
## RETN                 3          4         12          5          4          0
## CCL25                1          0          5          0          0          0
## ICAM1             1394        965        570        599        744        636
## TYK2              1723        924        802        743       1723       1408
## SMARCA4           4331       1358       1779       2043       3099       3312
## ACP5              1775        893        822       1627       1387        605
## JUNB              4805       1535       3885       3439       4400       2320
## CYP4F22           4247        997       1028       4441       2480        561
## JAK3               192         61         90        109        398        177
## JUND              3736       2241       2240       2543       2556       3204
## CEBPA            11518       3779       4164       6264       7960       3951
## CEBPG             2969       1536       2167       1735       1801       1588
## ACP7              2834        130        175        400       1448         44
## ZFP36             2146        965       1131        841       1194        822
## TGFB1             2342       1341       1307       1345       1760       1228
## RPS19            30384      26587      39467      30946      31227      26552
## PSG2                 9          3          1          0          0          0
## FUT2               301         50        139        101        169        106
## NKG7                79         31         63         69         86         52
## ZNF415             141        133        205        165         54        144
## LILRB2              85         93         69         58        117         46
## LILRA5               1          8          8          1          5          1
## KIR3DL1              0          0          0          0          2          0
## KIR3DL2              1          2          2          0          0          1
## SMOX              1706        354        354        841        569        165
## BMP2               420        447        358        289        243        378
## GINS1              225        130        234        195        311        193
## PLCG1             3353       1761       1318       1392       2148       1731
## YWHAB            11194       7113      10369      11285       8199       7731
## PI3               8180         98       1229        691      25963         36
## MMP9               165         69        146        343        702        181
## CD40               379        222        574        406        586        564
## PFDN4              446        402        655        428        502        381
## BMP7              1716        756        659        836       1112        784
## RPS21             8975      12680      16714      14178      15627      18254
## MX1               4966        542       1051        711       1601        725
## PFKL              4385       2831       3619       4979       4229       4143
## IL17RA            1600        885        659        919        948        811
## UBE2L3            3003       1656       2552       2549       2373       1882
## TPST2             1011        499        755        681        788        522
## XBP1              4556       2557       5568       4479       3099       4875
## UQCR10            1026        849       1280       1583       1199        978
## SEC14L2            836        187        302        563        305        387
## APOL6             2107        555        855        872       1728        949
## APOL1              479        147        414        383        878        603
## TYMP              5229        478       2179       2895       7053       2045
## BEND2                0          0          0          0          1          1
## PHEX                23         38         33         16         41         25
## TIMP1             1187       1969       2162       2002       1075       1472
## FOXP3              256         36         69         71        338        108
## MSN              10739       6073      10658       7946       7630       6631
## PGK1             10445       7217      12537      11370       9508       7211
## LAMP2             6370       4848       5701       6551       4188       4421
## CD40LG              31          8         54         68         56         32
## IRAK1             4936       2088       2447       2907       2888       2483
## COX2             42486      28818      33164      40947      54631      73749
##             GSM5630014 GSM5630015 GSM5630016 GSM5630017 GSM5630018 GSM5630019
## TNFRSF9            259         20         38          6        122         12
## ENO1             47473      17112      24119      14453      25604      16717
## PIK3CD             830        562        186        286        225        161
## PGD               6906       3407       2270       2134       3525       1970
## MTHFR             1282       1080        364        538        775        327
## TNFRSF1B          3013       1109        830        734        831        364
## PINK1             2632       2795        758       2476       1319       1606
## IFNLR1             554        253         91        133        238         69
## RUNX3             1304       1056        376        546        463        380
## SH3BGRL3         14766       4826       4716       6161       6005       3239
## CD52              1664        467        616        353        326        243
## IFI6             39656       1333       9966      18562      17207       1059
## ZC3H12A          12568        694       1429        221       8014        410
## UTP11             3555       1133       1577       1164       1978        928
## JUN               2656       2018        618       1169       1620       1288
## KANK4               24        131          2        148         10         11
## EFCAB7             382        340        138        180        138        189
## IL23R               27          5          6          0          9          0
## ADGRL2            2339       1182        444        799       1518        514
## GBP3               348        213        799       1175       1147        399
## GBP1              6544        687       2214       1266       4668        588
## GBP5              1701        201        169        203        483         38
## TGFBR3            1347       3670       1148       2826        861       1339
## VCAM1             1233        488        477        473        441        463
## PTPN22             526        112         68         81        182         21
## CD160               25         37         12          9          4         10
## FCGR1A             209          7        216         19        120         22
## MCL1             16651       6543       3659       5066       9750       3308
## CTSK             20778      30584       7645      37129      23262      16584
## RORC               197       1039         53        578         89        349
## S100A9         1539675        800     248022       1496     542849       7732
## S100A12           8999          0        873          0       5233          3
## S100A8         1411779        916     263285        288     466727       6388
## IL6R              1532        937        438        654        667        292
## RIT1              2853        968        678        767       1056        555
## BGLAP               30         32         18         11         17         15
## IFI16            13183       3350       4567       4025       7480       1815
## AIM2               304         32         58         47        216          6
## CRP                  0          1          2          0          2          0
## FCGR2A            1305        386        569        387        662        234
## HSPA6              625        166        192        130        225        156
## FCGR3A            1465         83        467        154        765         91
## SELL              1075         64        249         90        195         34
## GLUL             52821      13668       7784      13393      29472       8995
## PTGS2             1751         29         22         52        122         92
## CRB1                 0          9          4          6          0          0
## KDM5B             4137       2585        826       1426       2206        864
## IL10               139         54         20         52         50         13
## YOD1              5015       1137       1482       1367       3666        739
## HHAT               229        198         85        141        145        111
## TRAF5              356        647        199        272        170        167
## NLRP3              193         88         73         98         69         33
## LINC01250            1          0          0          0          0          1
## RPS7            124264      57413      38700      39422      36035      45195
## RSAD2             2620        160        646       1348       2985        157
## FOSL2             8198       4449       1584       2585       4218       2010
## REL               3381       1508        901        806       1503        434
## TGFA              7442        918        592        832       4981        543
## DYSF               619        408        270        238        324        274
## HK2               5319       1305        786        603       3282        435
## CD8A              1125        154        135         93        228         88
## CD8B               396         68         70         66        115        104
## EIF5B             6629       5031       4472       5424       3888       2747
## IL1R1             4656       3913       1697       2426       2897       1432
## RGPD6              505        734        206        412        308        238
## IL1A               294         44          4         87        298         65
## IL1B              3780         35         12         25        669          9
## IL37               502       1396        256       2105        214       1023
## IL36RN           38542        942       5356       2118      31989       1934
## IL1F10              94         71         81        201        134        218
## IL1RN            13352       1481       1235       1503       7690       1101
## NMI               4680        898       1540       1321       2527        879
## TNFAIP6            759        282        145        322        285        119
## IFIH1             3153        684        979       1343       2143        367
## SCN1A               13         15          3          6          1          1
## ABCB11              55         99          1         35          6          5
## RBM45              359        228        189        171        257        128
## FRZB               387        704        364        918        116        700
## TFPI              1145       1444        454       1387        720        618
## STAT1            16232       2932       4601       7495      11793       1698
## NABP1             1913        413        251        254        864        143
## SF3B1            11847      11322       3746       5127       5304       2985
## CASP10            1492        615        281        400        809        179
## CD28               504        104        190         66        117         38
## CTLA4              298         50         58          9         96          7
## ICOS               347         52         55         17         81          3
## NDUFS1            6604       4819       2020       2111       3492       1691
## CXCR2             1279        122        305        103        573        119
## IRS1               561        962        177        675        304        446
## CCL20              527         13         58          2        330         28
## ATG16L1           1343       1139        439        510        645        425
## GPR35               72         60         38         14         26         25
## PDCD1              220         24         19          6         52          7
## PPARG              282        908        106        564        183        220
## RPL15           127223      71375      39722      54064      41499      63711
## EOMES              137         62         23         10         24         10
## CX3CR1             376        214        159        225        115         41
## ACKR2              609         67        129         34        613         39
## CCR2              1139        369        312        341        293        189
## CCRL2              273         39         28         37         45         16
## TLR9                59         17          4          7         16          7
## ARHGEF3           2464       1206        907       1103       1229        749
## ADAMTS9            283        189        186        209        186        115
## TMEM45A          55388      13697      14895      11875      24181       9615
## CD80               134         12         11          3         40          3
## CD86               871        300        233        387        339        140
## MIX23             1351        397        701        397        565        304
## PLS1               489        170        148        119        296        127
## PTX3               101        105        307         35         89         31
## GOLIM4            1522       2023        783       2080       1081       1122
## MYNN              2368       1086        699        856        976        707
## TNFSF10          19223       3746       2545       3701       6042       2651
## ADIPOQ             202        552        272       3909         72        667
## SPON2              463       1513        246       1014        648        843
## S100P            12849       1956        617        351       4472       1286
## WDR1             14165       6206       6862       5606       9039       5836
## CD38               154         18         33          8         74          5
## PPARGC1A           105        845          8        207         54        234
## TMPRSS11B            0          0          0          0          2          0
## CSN3                 0          0          0          0          0          0
## ALB                  0          9          5          0          0          0
## CXCL8            88601          6         10         12       5286          1
## CXCL2              427         14         17          4        169         25
## AREG              1052        129        125         47        574         45
## CXCL10            2211         45        275         32        644         66
## CXCL13            1077          1         69          1        324          0
## SPP1              1152        178          5        276         73         16
## HERC6             4114        295        930       1562       3529        167
## NFKB1             4476       1870       1147       1330       1936        887
## SEC24B            1692       1495        609        875        714        441
## EGF                  8        121          4         75         18         39
## IL2                  7          3          2          0          6          0
## IL21                38          2          2          0         20          0
## IL21-AS1            12          0          0          0          3          0
## SLC7A11            717         28        165         65        352         43
## IL15               375        165        123        125        114         68
## EDNRA              615        412        264        497        495        398
## TLR2              1293        470        226        170        346         77
## FGB                  0          0          0          0          0          0
## DDX60             4396       1080       1273       2210       2982        333
## SPCS3            10404       3310       3735       3392       4928       2648
## TLR3               394        243        138        285        187        114
## OSMR              2458       1004        760        564       1446        390
## GZMK               575        136         90         49         61         26
## GZMA              1054        186        184         98        290         73
## ANKRD55             17         15          3          8          8          5
## CENPK              765        131        338         99        277        106
## CAST             16513      11062       5843      10730       7214       6191
## ERAP1             4575       3441       1279       2441       1898       1461
## ERAP2             2951       1277        125        143        142         49
## TNFAIP8           4877       1392       1134       1503       1363        902
## CSF2                39          9          1          3         17          0
## IL5                  0         13          2          0          0          0
## IL13                12          1          1          1          8          1
## IL4                  7          3          1          1          0          1
## CD14              3485       1656       1753       1328       1596       1099
## CSNK1A1          28456       8025      10987       8753      18434       6992
## PPARGC1B           800        358        234        136        304         91
## TNIP1             9676       2949       2047       3500       5478       2179
## ATOX1             3719        934       1041        915       1427        667
## FAXDC2            2428       3860        427       1783        758        695
## IL12B               96          1          6          0        147          0
## MIR146A              9          5          1          1          7          0
## PDLIM7            1501        898        601        714        715       1584
## SERPINB1         19259       1862       1819       2160      12501       1260
## SSR1              8448       3630       2966       3626       4570       2154
## CD83              1591        216        289        179        438        163
## SOX4              1382       1619        522       1004        584        750
## CMAHP              303        902        180        641        197        268
## HLA-A            67374      23278      24796      28564      28643      19757
## HLA-C            81016      27748      21600      32602      26871      18181
## HLA-B           114699      31894      44690      48593      47652      27234
## MICA               835        792        291        444        337        282
## LTA                 41         31         15         14          7         10
## TNF                287         73         63         43         92         30
## HLA-DRB1         10305       3516       5678       7006       8364       5875
## HLA-DQB1          2522        626       3374       4505       4303       2780
## PPARD             5478       1429        871        929       3580        606
## CCND3             3164       1512       1093       1282       1540        807
## VEGFA             2161       1681        307        484       1086        393
## RUNX2              215        129         48         66         72         38
## IL17A              242          0          6          0         63          0
## IL17F              133          0          8          0         64          0
## PRDM1             5201        672        814        489       2583        253
## ATG5              2819       1383       1092       1304       1197        934
## TRAF3IP2          2382       1093        810       1134       1435        802
## NCOA7             4586       1350        953        923       2458        556
## SGK1             13883       2990       2257       1713       5046       1736
## IFNGR1           21029       4469       3910       4083       8149       3100
## TNFAIP3           1789        601        325        378        581        312
## SOD2             41117       8213       7370       5621      20906       5147
## LPAL2               21         19          4          2          9          3
## PLG                  0          4          1          3          4          0
## CCR6               360        148         73        140        138         49
## RAC1             19180       7896       7875       9349       9838       5648
## ZNF316            1464       1589        416        870        534        462
## AHR               8196       4095       3821       3132       3294       1731
## IL6                 23          4         13          1         23         11
## TOMM7            10434       8953       4319       6175       3541       4851
## CYCS             24315       5152       9080       3956      11212       4036
## AQP1             11551      14760       6569      14375       8720      12557
## NT5C3A           11971       1345       2210       1550       5362        948
## EGFR              5238       7785       1503       3331       2216       1531
## CD36              9082       5258       3166       5365       9025       2489
## SAMD9             4165        289        540        489       3049        169
## SERPINE1           181         80        374        137        390        118
## CUX1              2887       1639        723       1499       1521       1043
## PSMC2            10176       3716       4070       4300       5046       3046
## NAMPT            43858       3569       5676       2879      28428       2373
## HYAL4             1155         39         94         19        462          7
## LEP                 59        176         48       1318          1         19
## CALD1             7401      10280       5699      12328       4981       9887
## BRAF               870       1089        266        711        339        318
## EZH2              1770        653        480        324        762        247
## DNAJB6           20576       4756       4637       4678      11742       4278
## CSMD1               51         70         13         30          0         17
## CTSB             49053      13886      15502      17136      25686       9168
## EGR3              2251       1245        533        813       1221        570
## TNFRSF10A          768        250        228        138        440        114
## BNIP3L           13939       6964       3065       5224       7469       3011
## DUSP4              890        959        216        711        402        369
## NRG1               367        237        213        183        175         80
## RPL7            144299     101431      51753      76548      58194      83665
## IL7                430        246        221        303        222        161
## GEM                533        382        185        277        459        357
## MYC               4405       1101       1340        785       2873        924
## GPT                298       1276         63        262         80        274
## JAK2              2030       1273        538        974        786        477
## CD274             1076         80         78         72        903         22
## IL33              8727       3917       2198       2576       2482       2069
## LURAP1L-AS1         16          9          4         13          2          1
## LURAP1L           1153        607        421        553        507        558
## TTC39B            5150       2522       1071       1109       2671        688
## IFNA1                0          0          0          0          0          0
## TEK                450        568        155        232        262        208
## TRBV20OR9-2          0          1          0          0          0          2
## TOMM5             6087       2072       2827       1972       2325       1561
## ANXA1            66900      13912       9473      19378      36947       8879
## ERP44             3562       1654       1428       1659       1769       1106
## ZNF483              65        299         84        146         33         82
## TNFSF15            144         51         19         16         69         29
## TLR4              1283       1371        525       1437        787        594
## PTGS1             4718       4963       1984       4020       2396       2437
## HSPA5            26996       9439      11984       7461      17800       6077
## FNBP1             3456       2569       1196       1903       1679       1373
## CARD9              348        169         77         87        149         85
## TRAF2              906        426        207        248        308        255
## CLIC3             3552        813        977       1197       1721       1360
## IL2RA              331         65         73         37        105         20
## GATA3             2300       3238       1140       2844        616       1128
## VIM              34118      51201      24339      66123      21959      34265
## CREM              1553        668        572        610        638        485
## DKK1                 9         77         54         85         93         54
## MBL2                 0          0          0          0          0          3
## SAR1A             6632       4367       2506       3819       3462       2340
## PRF1               547         67         77         58        215         41
## ZMIZ1             3103       3194        748       1665       1381       1045
## IFIT3             5532        820       2363       4654       4682        803
## TALDO1           12665       4935       3951       4098       5842       3279
## IGF2               532        464        166        345        148        262
## INS-IGF2           509        423        154        322        133        246
## IGF2-AS              1          2          0          1          3          0
## INS                  0          0          0          0          0          0
## STIM1             2869       2899        988       1980       1671       1276
## TRIM22            7213       2105       1525       2635       5002        674
## PTH                  0          0          0          0          0          0
## SAA1              1868        464        142        734        488         62
## SLC1A2              77        150         12         41         85         32
## FOSL1              400         11        144         27        531         22
## CCND1             2976       6881       1845       5839       1374       2697
## JRKL               302        497         87        199        151         98
## MMP7               432       2092        112        462        255        413
## MMP1               219          8         77         11        118          8
## MMP3                91         10         15         11         16         20
## CASP1             5460       1309       2198       2047       2992       1495
## DLAT              2063       1257       1032        806       1371        796
## IL18              6224       4310       3318       5509       1530       2425
## CD3E              1138        239        295        121        277         86
## MCAM              3047       2551       2259       2578       1738       4082
## WNK1              5660       7301       1660       4825       2586       2239
## TNFRSF1A          9108       3515       2554       3001       4922       2681
## GAPDH            82652      26742      41128      27718      43730      36899
## CD4               2651       1466        944       1726       1337        791
## SLC2A3            2511        409        283        339        337        183
## CLEC4D              63          0          5          2         13          4
## KLRB1              338        100         60         25        107         43
## CD69               552        174        108         76        140         91
## CLEC2B            7694       3507       2567       4078       2160       2772
## OLR1               148          3          3          4         15          3
## ABCD2               76         87          9        102         32         33
## LRRK2              719        653        166        514        299        290
## VDR               2117       1598        587       1008       1001        427
## TMBIM6           34276      21936      11034      17497      18560      12756
## PFDN5            26329      16453       8669      12312       7656      11325
## SP7                  0          6          0          0          0          1
## MUCL1             3803       8236        177       3392       1061       5434
## CD63             32632      23661      16206      30551      16505      20120
## SUOX              3155       2627       1042       2265       1585       1429
## RPS26            47689      18510      10876       5972      15060      14300
## RPL41           293694     152143     103169     130723      87204     115565
## IL23A              152         12         13          7         76          9
## DDIT3             1085        895        375        573        262        397
## IFNG                77          5          7          0         30          0
## IL22                30          0          1          0         71          0
## LYZ              28776       3311       6912       4478      14828       5151
## CAPS2               77        178         34         94         23         61
## SYT1                12         54         12         61          1         16
## BTG1             19550       7064       4875       7563       6565       5930
## HCAR3             4787        241        154        288        904        134
## GJB2            122883       2091      11571       1004      80353       2078
## GJB6             31307       1372       4802       1168      22654       1763
## TNFSF11             30         12         10          4          4          2
## TPT1            553032     225783     138123     144320     183432     199137
## LMO7              2711       1450        862       1057       2500        645
## TNFSF13B           876        347        409        476        369        226
## LAMP1             8929       7387       2968       5894       4499       3180
## PSME2             9157       1813       3590       2685       3750       1544
## GZMB              1284         27         96         22        654         15
## RPL36AL          16796       7350       6433       8092       6700       4027
## PYGL              6087       1631       1871       1833       3763        998
## HIF1A             6254       2631       1779       1516       4515       1412
## FOS               1196        522        469        272        869        390
## JDP2              1208       1592        737       1612        801       1025
## NOXRED1             37         58         11         19         13          9
## SERPINA1          1930         88        293        112       1050        212
## CDC42BPB          4020       3635       1007       2549       2189       1315
## PLA2G4D          25273        510       1127        166      14451        203
## TRIM69              44         23         26         38         41         18
## SLC51B              33         53         23         38         26         77
## SMAD3             1801       2432        581       1654        720        688
## CYP1A1               1          8          1          4        267        168
## AKAP13            3252       4739       1200       3338       1372       1250
## MEFV               359         25         45         16         94         11
## SOCS1              675        174        149        193        300         99
## ATXN2L            2322       2119        648        827        994        613
## CD19                39         10          4         10          7          0
## ITGAL              795        382        209        112        200         50
## ITGAM              526        584        240        517        219        215
## ITGAX             1329        244        133        112        124         65
## DNAJA2            8900       3290       2865       3238       4709       2711
## SIAH1             1227       1011        595        749        587        490
## ADCY7             2179       2256        536       1270        845        488
## NOD2              2495        442        449        294       1529        226
## CMTM2               90          7          4          0          9          0
## SF3B3             6872       3514       1816       2032       3734       1514
## PSMD7             9046       3441       3665       3599       4668       2841
## WWOX               538        121        300        161        270        169
## MAF               5815       6336       2030       4119       2450       2489
## SLC7A5            4562       1310       1780        465       3278        407
## CXCL16            2848        782        691        825       1442        637
## XAF1              3837       1215       1605       2377       3529        306
## CD68              3759       1907       1540       3652       2409       1131
## PER1              1492       3022       1180       2407       1065       2594
## NOS2              1748         11          4          5       1629          7
## TRAF4             1392        960        552        527        851        457
## CCL2              1956        274        425        304        811        373
## CCL5              1146        327        244        130        271        112
## CCL3               970         10         10          9         84          2
## CCR7               682         69        191         41        217         27
## STAT3            24557       6789       5060       4343      19163       3543
## SOST               492          0          1          7        678          8
## ITGA2B              44         22         16          6          8          3
## EFCAB13             57        197         14         35         13         32
## NPEPPS            5395       2918       1451       2163       3866       1326
## TBX21               52         17         13          5          6          6
## COL1A1           58448     145865      25171      33479      60303      24155
## MRPS23            4451       1511       1934       1493       1940       1294
## MIR21                4          2          2          1          2          1
## RPS6KB1           1971       1339        552        820       1239        565
## ACE                519        739        152        297        451        250
## ERN1              1181        793        220        324        546        205
## PRTN3                0          0          1          0          0          0
## PLIN5              699       1500        167        149        619         65
## RETN               126         75          5          7          4          8
## CCL25                0          4          0          0          3          0
## ICAM1             2184        933        427        546        800        292
## TYK2              2027       1835        517        701        962        603
## SMARCA4           3528       2553       1103       1490       1662        972
## ACP5              5056       1516        658       1285       2396        929
## JUNB             17602       2097       2697       1803       8472       2207
## CYP4F22           4878       1271        902        670       3288        562
## JAK3               799        204        155         59        167         47
## JUND              2479       2523       1624       2717       1668       2081
## CEBPA            11992       4793       4817       4847       6013       2917
## CEBPG             4791       1978       1706       1937       2970       1261
## ACP7             11807        263        482        132       6800        101
## ZFP36             5543       1192        640        806       2540        685
## TGFB1             3009       1513        901       1512       1205       1094
## RPS19           102946      43291      36856      40331      35363      40373
## PSG2                 5          3          2          1         15          3
## FUT2              2121        172         98         60        973         90
## NKG7               456         92         94         77        139         54
## ZNF415             317        482         47        136         48        128
## LILRB2             724        166        385        191        230         90
## LILRA5             188          5        196         26         58         15
## KIR3DL1              4          2          0          0          1          0
## KIR3DL2              8          0          3          2          0          0
## SMOX              1906        369        401        251       1636        199
## BMP2              1036        314        163        356        807        209
## GINS1             1226        260        561        219        640        264
## PLCG1             2917       2879        849       1194       1479        712
## YWHAB            21487      10270      10163      11928      11157       7069
## PI3             298441        160      10584        101     156252       1254
## MMP9              1416        134        164        244        269         89
## CD40              1242        590        442        605        526        386
## PFDN4             2211       1034        876       1021        675        773
## BMP7              1169       1072        757        896        856        512
## RPS21            73356      34706      25486      22105      19464      24816
## MX1               7385        818       2991       4967       7680        453
## PFKL              5111       4314       1803       2916       2695       2651
## IL17RA            1448       1297        473        783        560        272
## UBE2L3            7273       2796       2840       2811       3532       2245
## TPST2             2032        834        601        730        953        693
## XBP1             16801       6993       3642       4993       7720       4356
## UQCR10            6295       2629       2148       1712       2126       1472
## SEC14L2           1228        394        259        265        330        257
## APOL6             5062       1252       1330       1840       3984        563
## APOL1             6776        463        803        757       2589        196
## TYMP             30119       1838       4413       2309      14052       1182
## BEND2                0          0          0          0          2          1
## PHEX               160         50         18         66         60         24
## TIMP1             2417       2401       2497       3342       2611       1960
## FOXP3              440        117        106         32         95         34
## MSN              14451       7342       6938       8228       8277       7157
## PGK1             48135      13534      16511      11229      18452      10649
## LAMP2            14376       7441       3815       5520       5803       3708
## CD40LG              94         45         40         31         10          7
## IRAK1             5580       3315       2179       3416       3181       2044
## COX2             88595      66196      23164      45380      23436      24216
##             GSM5630020 GSM5630021 GSM5630022 GSM5630023 GSM5630024 GSM5630025
## TNFRSF9             96         18         21          4         15         19
## ENO1             37570      12977       9637      11113      14298      15243
## PIK3CD             250        185         81        117         83        210
## PGD               4939       3851       1319       1227       1419       1684
## MTHFR              630        446        157        336        198        342
## TNFRSF1B           709        401        189        317        197        319
## PINK1             1396       1710        479       1487        771       1257
## IFNLR1             201        140         60         86         82        134
## RUNX3              606        426        109        398        226        532
## SH3BGRL3          6500       2717       1772       3456       2796       2767
## CD52               781        420        796        219        579        265
## IFI6             12915        488       7394       1661        932        847
## ZC3H12A           5574        638        698        121       1120        319
## UTP11             1643        752       1059        843       1258        841
## JUN               1439       1018        264       1919        359        872
## KANK4                9         97          9         60         14          9
## EFCAB7             158        151         88        237        123        168
## IL23R               16          3          2          0          2          0
## ADGRL2            1144        788        269        388        302        297
## GBP3              1411        452        623        625        492        482
## GBP1              2775        508        545        733        469        540
## GBP5               383         71         97         70         59         57
## TGFBR3             707       1107       1126       2258       1113       1236
## VCAM1              544        417        339        328        329        203
## PTPN22             114         60         30         34         43         29
## CD160                8          9         13         11          7         10
## FCGR1A              51         10         32         14         33          6
## MCL1              6176       3277       1711       2395       2351       3508
## CTSK             10696       8379      10507      20973      10380       6973
## RORC               123        573         35        271        138        667
## S100A9          774869      19660     707780       1284     383484       3016
## S100A12           3671         22       2017         10        869          0
## S100A8          499912      15523     638183        952     339681       2336
## IL6R               590        343        188        310        213        398
## RIT1              1138        506        598        667        580        637
## BGLAP               21          9         10         16         13         18
## IFI16             4714       1410       1518       1363       1529       1758
## AIM2               189         18         21         13          9         15
## CRP                  0          1          0          0          0          0
## FCGR2A             331        133        135        168        113        109
## HSPA6              207         73        110        116         98         84
## FCGR3A             203         39         87         49        102         26
## SELL               238         30         49         40         36         27
## GLUL             34344       8002       8429       6340       9445       8277
## PTGS2               69         16         22         46         21         21
## CRB1                 0          0          0          4          0          2
## KDM5B             1712       1250        440        811        600       1312
## IL10                21         13         22          3         14          8
## YOD1              3287        757       1570        769       1122        671
## HHAT               137        134         35         57         95        123
## TRAF5              153        104         94        178        105        107
## NLRP3               54         24         37         40         21         26
## LINC01250            1          0          0          0          0          0
## RPS7             45555      46683      63300      45743      62370      40150
## RSAD2              914         40        317        170         75         53
## FOSL2             3369       2809        609       1200        817       2177
## REL               1179        744        654        370        687        531
## TGFA              3758        812        952        415        942        636
## DYSF               215        184         32        148         63        110
## HK2               2621        920        443        229        412        344
## CD8A               349         76         57         78        117        111
## CD8B               190         45         55        132         68         37
## EIF5B             2826       2156       1318       3015       2103       2859
## IL1R1             1631       1198        585        864        807       1430
## RGPD6              153        164         74        214        137        306
## IL1A                45         50         17         17         15         24
## IL1B               125         59         12          0         28         16
## IL37               358        462        111        695        324       1105
## IL36RN           25527        795       4944       1067       7372       1293
## IL1F10              92         26         53        118         36        133
## IL1RN             4393       1256        910        960        821       1648
## NMI               1571        561       1226        686       1036        511
## TNFAIP6            108         57        539        524        139         15
## IFIH1             1157        376        507        468        250        485
## SCN1A                3          2          0          0          2          4
## ABCB11              28         78          1          5          1         20
## RBM45              189         94         93        114        106        139
## FRZB               441        268        238        666        208       1175
## TFPI               473        380        479        673        309        437
## STAT1             8932       1703       1635       1548       1053       1677
## NABP1              634        216        138         98        142        123
## SF3B1             5241       3702       1727       2905       2741       3670
## CASP10             543        186        171        262        144        191
## CD28               203         49         44         16         82         19
## CTLA4              143         26         38          3         46         10
## ICOS               128         34         55          2         30          9
## NDUFS1            3535       2608       1397       1219       1630       1699
## CXCR2              654        148         83         38        153        110
## IRS1               183        410         98        477        150        241
## CCL20              128         22         56          0         53         26
## ATG16L1            602        529        267        430        347        461
## GPR35               27         13         16         31          8         11
## PDCD1               52          8         17          4          2         16
## PPARG               83        905        121        309         83        119
## RPL15            58598      57112      51282      55971      67837      57432
## EOMES               23         10          8          6         12         16
## CX3CR1             155        108         30         28         41        135
## ACKR2              325         12         73         66        207         12
## CCR2               281        142        138        112        150        216
## CCRL2               37         18         16         12         17         26
## TLR9                12          6         10          7          4          3
## ARHGEF3           1043        545        572        658        641        575
## ADAMTS9             90         82         37        157         57         47
## TMEM45A          30836      16909      12639       5538      18992      13019
## CD80                30          4         10          1          9          3
## CD86               284        165        133        121        135        161
## MIX23              494        320        525        412        351        204
## PLS1               188         64         62        121        104        132
## PTX3                52         17         53         48         55         23
## GOLIM4             696        515        411       1038        423        623
## MYNN               977        689        595        833        739        770
## TNFSF10           5776       2464       3780       2334       3356       2732
## ADIPOQ              14         99        193       1061         60         20
## SPON2              537        341        169        930        297        633
## S100P             2431        461       1801        300        712        223
## WDR1              8847       3428       2121       3808       2669       3941
## CD38                46          4         26         11          2          5
## PPARGC1A            37        204         30        146         92        218
## TMPRSS11B            1          0          0          0          0          2
## CSN3                 0          0          0          1          1          0
## ALB                  0          0          1          7          0          1
## CXCL8             1305         12        536         30         63          1
## CXCL2              139          5         54          3         16          1
## AREG               371        193        187         40        136         89
## CXCL10             356         63        150         50         48         92
## CXCL13             476         20         42          3        148         13
## SPP1                24         15          2         35         71         48
## HERC6             1689        150        569        131         98        211
## NFKB1             1500        783        345        633        533       1039
## SEC24B             692        598        363        625        362        526
## EGF                 12         56         10         35         25         45
## IL2                  3          2          8          3          1          2
## IL21                13          1          5          0          4          0
## IL21-AS1             6          0          2          0          0          0
## SLC7A11            287         36        114         26        113         42
## IL15               128         91        135         77         81         72
## EDNRA              280        157        122        302        150        105
## TLR2               265        197         85         96        119        147
## FGB                  0          0          0          0          0          0
## DDX60             1486        439        562        341        237        471
## SPCS3             4672       2529       2616       2201       2965       1869
## TLR3               104         90         51        109         57        114
## OSMR               876        359        279        322        288        283
## GZMK               117         48        108         41         46         65
## GZMA               311         86        280         89        136         70
## ANKRD55              9         12          6          1         11          8
## CENPK              282        120        278        105        261         95
## CAST              7701       4570       2394       5144       3409       6877
## ERAP1             1546       1251        649       1280        937       2389
## ERAP2               97         85        106         69         36         40
## TNFAIP8           1689       1040       1117       1175       1364       1435
## CSF2                 5          2         10          3         17          0
## IL5                  0          1          0          1          0          3
## IL13                 2          1          2          2          1          4
## IL4                  0          0          0          2          1          0
## CD14              1177        401        794       1241        536        372
## CSNK1A1          14995       5512       6097       5234       7323       6103
## PPARGC1B           347        242        108         84        129        144
## TNIP1             5127       1861       1072       1621       1371       1623
## ATOX1             1526        557       1120        627        940        564
## FAXDC2             952       2159        198        528        286        626
## IL12B               24          1          7          1          9          3
## MIR146A              3          1          2          1          3          1
## PDLIM7             580        269        213        684        432        371
## SERPINB1          4171        802       2343       1474       1692       1052
## SSR1              3817       2277       1578       1835       1663       2317
## CD83               488        201        164        120        154        164
## SOX4               673        651        283        973        444        645
## CMAHP              190        417        169        334        122        420
## HLA-A            30769      14370       9247      13771      14728      28915
## HLA-C            36450      16843      11792      14550      12072      21635
## HLA-B            53675      22243      18825      18866      15806      28691
## MICA               265        160        246        368        302        416
## LTA                 23         21          7          5          4          4
## TNF                122         63         36         29         51         43
## HLA-DRB1          8988       4464       5554       4999       2970       3164
## HLA-DQB1          7659       3706        680        842        478        822
## PPARD             3154        848        435        450        500        593
## CCND3             1270        673        448        631        681       1101
## VEGFA              825        665        146        306        303        316
## RUNX2               69         85         18         48         32         34
## IL17A               34          0          8          0         11          0
## IL17F               31          0         69          0         98          0
## PRDM1             2298        556        741        276        667        315
## ATG5              1091        820       1105        968       1030        841
## TRAF3IP2          1053        599        216        571        418        764
## NCOA7             1281        594        494        585        396        430
## SGK1              5068       1634       1503       1217       1841       1921
## IFNGR1            6677       3177       4284       2773       4157       2864
## TNFAIP3            522        370        140        273        159        319
## SOD2             13116       4559       4326       3055       5523       3459
## LPAL2                5          1          4          8          1          0
## PLG                  0          0          0          0          0          0
## CCR6               191        106         49         31         61        109
## RAC1              8194       4432       3547       4714       4792       6062
## ZNF316             451        552        118        434        181        426
## AHR               2273       2100       1931       2448       1872       1888
## IL6                 18          3          2          0          9          2
## TOMM7             4241       3793       4756       5568       5132       5403
## CYCS             12588       4187       7453       3055       6655       3202
## AQP1              7474       4187       3779      13154       4354       7726
## NT5C3A            6450       1024       3751        664       3245        672
## EGFR              1584       2707        558       1365        910       2696
## CD36              8026       2655       3420       1766       3731        860
## SAMD9             1421        151        370        163         69        148
## SERPINE1           131         54         62        112        105         47
## CUX1              1197        723        204        718        485       1098
## PSMC2             5921       2968       2693       2445       3555       3237
## NAMPT            12323       2828       6207       1543       5609       1977
## HYAL4              638         14        276          1        103          9
## LEP                  3         34         71        313         22         11
## CALD1             3326       2352       1478       5325       3935       3952
## BRAF               389        399        120        314        219        340
## EZH2              1088        409        297        252        346        360
## DNAJB6           10896       3641       3555       3033       5035       3670
## CSMD1               17         30          2         30         14         14
## CTSB             18056       7529       4698       6120       7195       7064
## EGR3              1675       1817        326        406        398        627
## TNFRSF10A          272        121        120         70         94        118
## BNIP3L            8212       5933       3637       3647       4247       3492
## DUSP4              420        574        120        224        150        337
## NRG1                86         88         10         59         64        179
## RPL7             67207      71451      50366      73437      73753      84404
## IL7                196        204        172        199        152        210
## GEM                479        139        107        252        198        131
## MYC               2069       1217        364       1241        534       1139
## GPT                224       1620         44         91        135        329
## JAK2               685        481        290        411        359        498
## CD274              281         32         52         14         66         27
## IL33              2104       1678       1973       1581       1378       2311
## LURAP1L-AS1          2          1          1          3          2          3
## LURAP1L            469        310        274        501        403        433
## TTC39B            2639       2361       1346        664       1181        720
## IFNA1                1          0          0          0          0          0
## TEK                135        106         55        120         48        191
## TRBV20OR9-2          0          0          0          0          0          0
## TOMM5             2614       1453       2842       1615       2521       1315
## ANXA1            22024       5453       6871      11874       5580       9477
## ERP44             1695        801        894        886       1053        880
## ZNF483              56         66         21         63         33         57
## TNFSF15             59         45          5          5         26         28
## TLR4               446        234        487        702        255        215
## PTGS1             2583       2493       1255       2307       1800       3871
## HSPA5            12710       6232       4546       3965       5566       4861
## FNBP1             1781       1065        493        939        793       1183
## CARD9              199        113         26         24         38         84
## TRAF2              404        283         85        155        141        372
## CLIC3             3077        919        707        733       1353       1627
## IL2RA              130         52         47          3         29          9
## GATA3             1054       2086        643       2261        893       3518
## VIM              20125      13875      12175      33509      12717      17579
## CREM               537        380        451        359        418        301
## DKK1                10         24         21         24         13         12
## MBL2                 0          0          0          0          0          0
## SAR1A             2883       1751       1713       2133       2118       2048
## PRF1               130         49         53         52         55         67
## ZMIZ1             1302       1297        293        907        415        918
## IFIT3             2116        364       1219        915        536        551
## TALDO1            7107       4849       3045       2536       3462       3348
## IGF2               186        112         85        407         59        104
## INS-IGF2           171        109         82        394         59         97
## IGF2-AS              0          0          0          0          0          1
## INS                  0          0          0          0          0          0
## STIM1             1405       1001        293        893        526       1439
## TRIM22            2837        621        901        745        462        672
## PTH                  0          0          0          0          0          0
## SAA1               548       1277        573        267        130         53
## SLC1A2              41         42         46        131         23         64
## FOSL1              218         30          7         18         11          7
## CCND1             1606       2614        492       2279       1072       5060
## JRKL                96        110         25         79         70        137
## MMP7               227        561        163        592        366        689
## MMP1               110          2         18          0         63          0
## MMP3                 1          4          5          7          3          1
## CASP1             2445       1017       1332        880       1406       1247
## DLAT              1281        754        446        538        567        636
## IL18              2847       2809       3149       3178       3432       3767
## CD3E               634        150         78         80        114        120
## MCAM              1324       1355        747       1530       1482        760
## WNK1              2033       2676        547       1801        996       2500
## TNFRSF1A          4220       1937       1081       1885       1713       2989
## GAPDH            55410      16880      22492      26363      24828      27284
## CD4               1263        625        229        561        344        541
## SLC2A3             356        175         78        220         94        112
## CLEC4D               8          3          0          0          7          0
## KLRB1              169         60         50         21         60         36
## CD69               204        130        120        175        106         56
## CLEC2B            2256       2021       4954       3120       4309       3078
## OLR1                18          4          3          3          0          0
## ABCD2               31         18         20         41         11         16
## LRRK2              248        225        134        268         77        168
## VDR                902       1043        143        370        212        769
## TMBIM6           15662      19549       5893       9035       8211      12515
## PFDN5             9477      10802      14793      12825      14027       9877
## SP7                  0          2          2          0          0          1
## MUCL1             2756        594       1542       2680       2442       4309
## CD63             14169      10531      15994      26368      15376      13365
## SUOX              1548       1577        331       1113        647       1516
## RPS26            20908      17177      21383      14707      10301       4631
## RPL41           113201     120865     146000     115881     155941     111490
## IL23A               54          5          8          5          8          7
## DDIT3              278        198        266        304        306        305
## IFNG                27          3         12          0          2          4
## IL22                16          1         12          0         19          0
## LYZ              15003       4624       9678       3079       7529       1821
## CAPS2               33         36         25         81         25         54
## SYT1                21         10          5         10          7         14
## BTG1              6322       4714       3876       4873       4524       6509
## HCAR3              790        221        181        121        263        256
## GJB2             44796       2772       9977        959       4406        972
## GJB6             19922       1443       5414       1216       3343       1226
## TNFSF11              9         18          0          1          5          3
## TPT1            212598     187659     246631     190402     281652     150539
## LMO7              2549        634        736        477        655        800
## TNFSF13B           320        215        340        192        295        108
## LAMP1             4218       3602        811       2723       1501       3785
## PSME2             4416       1439       2420       1364       1848       1526
## GZMB               344         13         84          8         35          4
## RPL36AL           6397       4474       4734       4672       5098       4006
## PYGL              1510       1065        863        999       1261       1033
## HIF1A             2440        879        732        978        868       1269
## FOS                867        732         80       1525        222        765
## JDP2               703        503        412       1309        554        814
## NOXRED1             14         14          7          9         14         17
## SERPINA1           833         96         97         91        105         48
## CDC42BPB          1593       1529        304       1196        510       1184
## PLA2G4D          11477        432       2108        117       1424        274
## TRIM69              40         11         37         15         35         18
## SLC51B              28         18         22         34         29         15
## SMAD3              623        663        252        820        262        873
## CYP1A1               4          3         24         31          6          5
## AKAP13            1143       1480        479       1328        652       1132
## MEFV                32         15         11         16          9         11
## SOCS1              185         76         74         48         30         38
## ATXN2L             889        846        150        573        223        604
## CD19                10          6          0          1          3          0
## ITGAL              285        136         51         58         60         40
## ITGAM              262        138        159        304         99        113
## ITGAX              142        138         31         44         52         39
## DNAJA2            4775       2252       2693       2252       2936       2600
## SIAH1              556        485        426        489        426        446
## ADCY7              931        644        244        513        285        425
## NOD2              1313        377        295        205        302        245
## CMTM2                1          1          0          0          4          0
## SF3B3             3504       2263        746        980        894       2252
## PSMD7             5071       2926       2391       2441       3142       2525
## WWOX               383        139        188        150         76        149
## MAF               2399       2334       1196       2737       1685       3000
## SLC7A5            2676       1554        431        172        274        519
## CXCL16            1237        512        236        310        295        528
## XAF1              1330        343        430        282        121        200
## CD68              1496        571        760       1164        644        544
## PER1              1838       1835        500       1143        677       1417
## NOS2               589          1          8          9          0          3
## TRAF4              734        581        319        524        618        601
## CCL2               514        287        291        213        432        256
## CCL5               348        158        144         73        133        111
## CCL3                57          7         13          9          9          3
## CCR7               269         68         80         19         83         43
## STAT3            13640       3866       2535       2205       3452       3193
## SOST               384          3          3          8          5        108
## ITGA2B              12          4          3          3          0          2
## EFCAB13             14         50         35         48         19         21
## NPEPPS            2937       1429        899       1207       1092       1428
## TBX21               20          7          2          1         12          0
## COL1A1           20243      25662       6687      26164      18324      19065
## MRPS23            1823       1027       2009       1366       1769       1059
## MIR21                2          0          0          1          1          0
## RPS6KB1            826        545        259        445        389        518
## ACE                222        227         87        229         95         92
## ERN1               414        278        103        141        147        231
## PRTN3                0          0          3          3          0          0
## PLIN5              607       1583        184         30         79         81
## RETN                 2          6         14         13         13          9
## CCL25                0          0          0          0          0          3
## ICAM1              637        194        167        222        206        216
## TYK2               835        734        175        513        221        593
## SMARCA4           1499       1238        326        770        505       1372
## ACP5              2520       1718        869        592       1000        734
## JUNB              9964       3418       1978       1367       2485       2788
## CYP4F22           3885       1368        516        323        684        769
## JAK3               258        118         58         40         38         65
## JUND              1370       1319        433       1653        796        956
## CEBPA             7541       4773       3032       2774       3643       4089
## CEBPG             2285       1252        866       1225       1311       1673
## ACP7              6755        444        940         71        588         84
## ZFP36             1990        832        270        604        423        625
## TGFB1             1160        592        286        985        425        862
## RPS19            48495      37483      44846      40991      52440      47595
## PSG2                15          1          2          0          1          1
## FUT2               792         59        182         24        196        102
## NKG7               174         45         55         26         48         17
## ZNF415             101        194         49        130        100        243
## LILRB2             138         51         99         72         32         22
## LILRA5              22          4         28         20         15          2
## KIR3DL1              2          0          0          0          0          0
## KIR3DL2              0          2          2          0          0          0
## SMOX              1116        263        315        185        472        155
## BMP2               608        171        148        247        101        348
## GINS1              489        203        266        186        284        153
## PLCG1             1631        994        299        672        437        714
## YWHAB            11307       6516       4012       6199       5501       7046
## PI3              99865        240      13235        102       8968        273
## MMP9               689        161         56         33         77         61
## CD40               469        243        235        248        360        455
## PFDN4              810        699       1462        955       1218        628
## BMP7               753        436        223        423        371        602
## RPS21            28960      27690      44577      28206      39415      22980
## MX1               2284        226        460        402        125        278
## PFKL              3138       3461        549       1885       1029       2436
## IL17RA             508        508        168        505        190        303
## UBE2L3            3509       1791       1594       1643       1950       1978
## TPST2              889        543        364        591        416        575
## XBP1              6672       4306       2845       3237       3616       2746
## UQCR10            2744       2134       2210       1376       2155       1411
## SEC14L2            571        299        155        189        194        147
## APOL6             2273        473        556        515        345        466
## APOL1             1201        220        153        198        162        183
## TYMP             17668       1942       1912        692       1239        780
## BEND2                0          0          0          1          1          1
## PHEX                85         27         62         15         34         25
## TIMP1             1076        712        699       1802        808        843
## FOXP3              209         87         24         17         26         47
## MSN               7382       3125       1480       4559       2956       4843
## PGK1             24123      11431      15441       9290      17116      10233
## LAMP2             5693       4604       2747       3397       3843       4406
## CD40LG              62         20          8          3         31         21
## IRAK1             3429       1560        660       1629       1082       1291
## COX2             20359      27200       9003      23684      14876      29334
##             GSM5630026 GSM5630027 GSM5630028 GSM5630029 GSM5630030 GSM5630031
## TNFRSF9             33          6         28         16          9         34
## ENO1             10687      14323      17343       7352       5292      10629
## PIK3CD              35        143        149        155         70         79
## PGD                883       2312       2287       1283       1293       1366
## MTHFR              129        327        179        197        159        164
## TNFRSF1B           161        272        506        443        198        227
## PINK1              325       1425        716        924        808        497
## IFNLR1              18         93        113        102         48         68
## RUNX3               94        554        469        347        194        169
## SH3BGRL3          1196       2709       3495       1948       1316       2123
## CD52               132        196        331        209        223        287
## IFI6              1010        810       2350        728        287       6851
## ZC3H12A            567        245       2409        100         90       1990
## UTP11              662        616        606        358        365        705
## JUN                138        627        556        715        332        356
## KANK4                7         38         15         11         17          3
## EFCAB7              50        155         38         47         90         47
## IL23R                4          0          1          0          0          1
## ADGRL2             194        487        311        444        310        325
## GBP3               256        238        335        256        232        554
## GBP1               757        334        635        378        219       1170
## GBP5                86         55        102         69         60        161
## TGFBR3             215        959        492       1364        457        257
## VCAM1              122        258        204        295        132        225
## PTPN22              34         26         46         39         34         52
## CD160                2         15          7          9          7          4
## FCGR1A              44          5         33          4          6         17
## MCL1              1419       2541       2634       2432       1658       2054
## CTSK              7680      13707       6568       8423       9030       4030
## RORC                20        454         65        235        227         45
## S100A9          239207       1230     242363        106        750     217771
## S100A12           1200          0       1175          2          0       1070
## S100A8          236857       1680     177369        165        970     208491
## IL6R               205        297        224        260        179        142
## RIT1               506        523        419        297        278        397
## BGLAP                3         10          6          3          4          6
## IFI16              769       1270       1842       1246        689       2665
## AIM2                23         14         45         16         10         56
## CRP                  0          0          0          0          0          1
## FCGR2A             168         86        166        175        117         92
## HSPA6              139         41        119         86         35        122
## FCGR3A              93         29         98         40         29        131
## SELL                47         38        116         47         33         72
## GLUL              5021       7025       8063       4411       3348       7172
## PTGS2               22         21         32         50          4         28
## CRB1                 0          2          0          2          1          0
## KDM5B              345        946        633        701        532        703
## IL10                25         14         13          7         16          1
## YOD1              1016        491       1211        685        691       1204
## HHAT                39        129         60         88         31         68
## TRAF5               44        136         59         95         61         61
## NLRP3                3         21         41         53         21         31
## LINC01250            0          0          0          0          0          0
## RPS7             28812      28010      18767      14089      18740      19735
## RSAD2               42         49         85         94         49        544
## FOSL2              422       1682       1777       1879       1052       1138
## REL                254        451        491        403        241        460
## TGFA               541        573        930        287        493       1033
## DYSF                44        140        154        197         52         63
## HK2                353        493        992        364        269        559
## CD8A                96         52        203        229         93        187
## CD8B                56         53         89        107         58         81
## EIF5B              831       2389       1916       1946       1061       1015
## IL1R1              643       1304        792        872        736        646
## RGPD6               68        216         69        136         97         73
## IL1A                43         63         12         20         48          9
## IL1B                23         14         39          6         13         20
## IL37               167        615        145        791       1004        186
## IL36RN            4060        626       6898        998        721       6941
## IL1F10              95         94         18        101         61         38
## IL1RN             1067       1038       1178        674        855       1459
## NMI                681        409        586        331        253        764
## TNFAIP6            235        101         54        130         42         45
## IFIH1              123        255        255        208        122        576
## SCN1A                0          0          1          1          0          1
## ABCB11               0         22          1          2         15          5
## RBM45               51         89         62         79         33         87
## FRZB               179        648        211        309        150        113
## TFPI               201        367        204        377        300        235
## STAT1             1439       1172       2088       1440        915       3942
## NABP1              149        129        145         60         94        114
## SF3B1             1333       3397       1917       2109       1629       1824
## CASP10             108        160        141        143         70        164
## CD28                28         35         59         38         27         44
## CTLA4               16         16         23          4          8         36
## ICOS                12         13         36          6          9         48
## NDUFS1             925       1771       1301        946        891       1298
## CXCR2               99         67        231         37         40        262
## IRS1                93        261        107        270        123         52
## CCL20               33          4         56          0          1        147
## ATG16L1            195        403        218        224        209        149
## GPR35                9         12         12          5          2          6
## PDCD1                7          8         24         12          1         13
## PPARG               44        344         53         94        301         27
## RPL15            24873      40067      24809      22465      25085      22858
## EOMES                6          2         15         35          8         10
## CX3CR1              17        105         80        175         76         40
## ACKR2               49         14         98         22          4         76
## CCR2                54        214        162        217        151         78
## CCRL2               29         21         10         10         20         13
## TLR9                 1          6         11          5          1          1
## ARHGEF3            308        549        555        510        248        496
## ADAMTS9             41         82         45         82         40         16
## TMEM45A           9435      10999      10985       7152       8571      13480
## CD80                13          6          9          2          0          8
## CD86                92        139        114        139        105        123
## MIX23              295        184        186         93        132        210
## PLS1                38         81         64         62         34         74
## PTX3                33         33         29         19         14          6
## GOLIM4             204        734        412        750        325        213
## MYNN               441        535        301        281        288        334
## TNFSF10           1827       1470       1926        857        831       2423
## ADIPOQ             124        237        112        173         61          0
## SPON2              153        502        359        474        185        134
## S100P             1353        611       1120        141         60        491
## WDR1              2169       3767       4923       2864       1609       2618
## CD38                 5          3         30          7          1         17
## PPARGC1A            26        454         34         77        121          8
## TMPRSS11B            0          0          0          0          0          0
## CSN3                 0          0          0          0          0          0
## ALB                  1          0          0          0          0          0
## CXCL8              386          0        215          3          3        270
## CXCL2               39          0         19          2          1         52
## AREG               130         77         86         10         22        125
## CXCL10             168          8        123         44         25        152
## CXCL13             127          6         44          1          2        317
## SPP1                10          4          2         13          4         52
## HERC6               76        151        230        124         66        958
## NFKB1              268        661        720        614        347        525
## SEC24B             163        455        314        379        236        266
## EGF                  2         30          6         27         10          2
## IL2                  0          0          1          0          3          1
## IL21                 0          1          3          0          0          6
## IL21-AS1             0          0          2          0          0          4
## SLC7A11            119         16         93         29          9        134
## IL15                35         69         60         41         50         47
## EDNRA              103        256        152        258        105        127
## TLR2                61        178         94         82        108        115
## FGB                  0          0          0          0          0          0
## DDX60              122        311        249        396        229        824
## SPCS3             2127       1600       1719       1303       1078       1644
## TLR3                31         54         62         99         57         66
## OSMR               167        391        325        227        173        308
## GZMK                41         22         79         91         23         82
## GZMA               111         28        119        129         37        140
## ANKRD55              0          3          7          2          2          3
## CENPK              104         66         82         44         50        107
## CAST              2264       6039       3617       4492       2696       3179
## ERAP1              414       1439        773       1114        602        637
## ERAP2              179        434        779        890        135        765
## TNFAIP8            671        664        683        461        599        805
## CSF2                 0          1          2          1          3          5
## IL5                  0          1          0          0          0          0
## IL13                 0          4          1          1          0          0
## IL4                  0          1          0          2          0          0
## CD14               440        444        784        889        337        309
## CSNK1A1           5291       4449       6274       3873       2498       6057
## PPARGC1B            31        174        126         74         40        118
## TNIP1              841       1651       2371       1287        885       1674
## ATOX1              507        512        607        323        244        703
## FAXDC2             142       1420        388        611        835        265
## IL12B               12          1          3          0          1          7
## MIR146A              2          0          2          0          0          1
## PDLIM7             154        451        418        269         98        180
## SERPINB1          1891       1003       1673        717        406       1226
## SSR1              1314       1964       1678       1567       1038       1390
## CD83               142        109        182         98         59        154
## SOX4               173        670        420        509        346        213
## CMAHP              144        325         40        140        247         37
## HLA-A             7093      11439      18276      14444       6461      11896
## HLA-C             4968       8412      21325      15804       8280      16970
## HLA-B             7940      14594      25613      16977      11789      19611
## MICA               179        287        112        109        130        122
## LTA                  5          6         14         16          2          8
## TNF                 19         18         43         40         14         37
## HLA-DRB1          3229       5597       4924       4670       5064       4975
## HLA-DQB1           544       1410        781        729        592        751
## PPARD              399        636       1312        450        374        827
## CCND3              246        765        667        553        299        436
## VEGFA               93        582        469        266        138        204
## RUNX2               18         60         35         48         16         19
## IL17A                8          0          8          0          0         15
## IL17F                3          0         11          0          0          8
## PRDM1              340        282        822        287        285        804
## ATG5               572        701        414        338        349        481
## TRAF3IP2           308        610        529        486        275        402
## NCOA7              437        444        484        334        226        511
## SGK1              1446       1545       1765        616        502       2021
## IFNGR1            2970       1875       2102       1353       1331       2402
## TNFAIP3            120        234        210        283        136        152
## SOD2              6032       3715       4397       2013       1900       4636
## LPAL2                3          3          2          1          3          1
## PLG                  0          7          0          0          1          0
## CCR6                23        104        102        121         50         48
## RAC1              2200       4598       4904       3838       2694       3584
## ZNF316              67        397        258        340        190        118
## AHR                769       1738       1083       1300        688       1135
## IL6                  6          2          3          0          0          8
## TOMM7             1854       3257       1837       2022       2629       1972
## CYCS              6908       2977       4287       1489       1433       4031
## AQP1              2045       6446       5403       9081       2531       2315
## NT5C3A            2040        587       2045        482        588       2533
## EGFR               246       2262        882       1740       1077        619
## CD36              3164       1921       3785       1342        958       4953
## SAMD9              122        103        270        125         77        646
## SERPINE1           132         43         42         82         20         35
## CUX1               243        714        632        774        292        342
## PSMC2             2149       2418       2097       1459       1433       1979
## NAMPT             9003       1798       5075       1049       1077       5074
## HYAL4              165         28        144         14         10        476
## LEP                  7         59         84         87          1          0
## CALD1             1505       5162       2711       3254       1853       1350
## BRAF               129        337        182        220        205        122
## EZH2               318        265        292        130        162        337
## DNAJB6            4447       2701       4122       1910       1887       3504
## CSMD1                0         31          3          4          7          7
## CTSB              6404       9202       8807       6061       4297       6546
## EGR3               156        616        410        407        420        418
## TNFRSF10A          119        117         91         54         49         94
## BNIP3L            2215       4351       3399       2273       2908       2748
## DUSP4              150        380        156        198        173        119
## NRG1                43         77         29         83         26         38
## RPL7             32952      64734      32426      35977      39900      28911
## IL7                 64        107         64         90        126         84
## GEM                116        133        171        256         79        120
## MYC                332        506        815        424        253        626
## GPT                 22        629         72        129        282         60
## JAK2               116        511        232        360        271        392
## CD274              102         23         86          7         12         85
## IL33              1211       1241        921        501        803       1025
## LURAP1L-AS1          4          1          1          0          4          0
## LURAP1L            100        299        228        256        149        121
## TTC39B             691       1222        727        380       1012       1087
## IFNA1                0          0          0          0          0          0
## TEK                 30        122        130        140         44         52
## TRBV20OR9-2          0          0          0          0          1          0
## TOMM5             1509        950       1062        509        707        927
## ANXA1             8105       7381       4489       5273       3484       2876
## ERP44              571        723        736        616        502        565
## ZNF483               8         70         16         29         28         16
## TNFSF15             13         24          9          5          9         25
## TLR4               453        361        197        435        325        136
## PTGS1              528       1922       1354       2135       1574       1444
## HSPA5            12090       4535       5619       3772       2179       4444
## FNBP1              316        876        762        909        527        549
## CARD9               15         64         82         63         31         25
## TRAF2               69        233        227        143        115        108
## CLIC3              619        835       1410        619        340        875
## IL2RA               17         19         27         25         13         25
## GATA3              137       1596        550       1313       1071        308
## VIM               8677      22567      13689      22929      13179       7536
## CREM               399        324        196        154        141        197
## DKK1                34         36          7          6         22          6
## MBL2                 0          0          0          0          0          0
## SAR1A             1297       1747       1074       1144        869       1035
## PRF1                22         23         60         61         19         37
## ZMIZ1              161        901        754        984        342        288
## IFIT3              313        329        572        425        261       1299
## TALDO1            1774       3186       2970       1736       2012       2453
## IGF2                49        101         97        133         77         51
## INS-IGF2            48         96         82        120         66         46
## IGF2-AS              1          0          0          0          0          0
## INS                  0          0          0          0          0          0
## STIM1              277       1173        832        974        426        478
## TRIM22             515        527        463        516        440       1349
## PTH                  0          0          0          0          0          0
## SAA1               182        178        112         17        218        147
## SLC1A2               3         45          5         26          9         41
## FOSL1               66         12         67          6          5         33
## CCND1              340       2798       1232       2871       1137        628
## JRKL                12        103         45         66         55         30
## MMP7               223       1848        199        191         97        195
## MMP1                37          4          9          8          0         45
## MMP3                12          6          3          3          0          6
## CASP1              776        752        978        645        474       1107
## DLAT               235        603        519        407        292        490
## IL18              1776       2820       1056       1584       2469       1173
## CD3E                74         73        250        185         95        193
## MCAM               725       1405       1069        770        530        501
## WNK1               330       2497       1095       2353       1323        712
## TNFRSF1A          1258       1867       1937       1470        901       1410
## GAPDH            16855      24938      26706      13429       9020      19246
## CD4                154        472        616        944        419        350
## SLC2A3              83        136        150        145         55        131
## CLEC4D               6          1          3          0          1          5
## KLRB1               96         42         63         19         23         46
## CD69                49         40         57         42         32         57
## CLEC2B            1223        988       1116        927       1088       1732
## OLR1                 8          0          2          0          4          7
## ABCD2                6         15         13         13         21         13
## LRRK2               38        163         89        163        122         91
## VDR                132        664        403        435        280        225
## TMBIM6            5294      13586       7518       6873       8750       5797
## PFDN5             5694       7042       3872       3612       4618       3893
## SP7                  0          3          0          0          1          0
## MUCL1             1073       3956       1947       1412        143        439
## CD63              9948      13065       7745       8356       7554       4894
## SUOX               340       1371        740       1048        771        551
## RPS26            10051       9879       8167       5030       2305       4090
## RPL41            61177      78308      44035      38123      48044      51266
## IL23A                4          7         13          3          0         13
## DDIT3              287        281        104        135        147         95
## IFNG                11          0          3          5          1         10
## IL22                 2          0          6          0          0          3
## LYZ               3918       2357       6648       4465       2724       3984
## CAPS2               26         53         15         12         20         11
## SYT1                 7          9          1         12         16          2
## BTG1              1958       3775       4202       3160       3341       3508
## HCAR3              143         59        216        109        111        241
## GJB2              9677       1948      19498       1039        524      13975
## GJB6              5792       1328       9688       1150        490       5550
## TNFSF11              1         17          8          9          9          6
## TPT1            133918     121748      91598      69548      83508      94538
## LMO7               282        626        794        438        252        937
## TNFSF13B           137        141        162        131        147        128
## LAMP1              692       2987       2622       3386       1776       1605
## PSME2             1382       1005       1621        729        637       1552
## GZMB                84          5        151         35          9         78
## RPL36AL           2565       3421       3161       2583       2331       3030
## PYGL               516        684       1314        521        413        867
## HIF1A              833       1154       1179        817        339        906
## FOS                 35        227        111        422        210        925
## JDP2               209        678        399        539        310        303
## NOXRED1              1          4          3          7          3          7
## SERPINA1           148         45        211        115         35        154
## CDC42BPB           239       1124        812       1032        488        450
## PLA2G4D            572        139       4116        187        100       3091
## TRIM69               8          6         16          3          5         11
## SLC51B              16         46          8         12          9          6
## SMAD3              199        622        348        495        407        243
## CYP1A1               1          6          0         65         10          0
## AKAP13             249       1159        587       1278        571        353
## MEFV                 4          4         12          9          4          3
## SOCS1               35         45        114         40         47         69
## ATXN2L             132        522        367        346        253        229
## CD19                 2          0          0          0          0          0
## ITGAL               12         50        100        134         36         72
## ITGAM               61        161        138        241         93         86
## ITGAX               10         70         53         66         31         43
## DNAJA2            1959       1842       1681       1272       1091       1774
## SIAH1              268        365        309        245        187        236
## ADCY7              116        427        348        472        243        170
## NOD2               217        197        444        168         96        308
## CMTM2                0          1          1          1          0          1
## SF3B3              624       1539       1335       1139        775       1018
## PSMD7             1878       2141       2100       1433       1344       1866
## WWOX               148        205        307         90         74         66
## MAF                468       1730       1505       1758       1003        690
## SLC7A5             348        489       1774        330        195        768
## CXCL16             191        364        702        427        182        401
## XAF1               114        166        293        153        104        710
## CD68               492        736        681        947        571        546
## PER1               288       1024        830       1237        524        344
## NOS2                21          5        184          3          1        104
## TRAF4              302        537        356        151        157        210
## CCL2               212        164        226        102         56        235
## CCL5                59         36        261        255         90        221
## CCL3                11          2         10          5          9         21
## CCR7                15         33        108         37         15         94
## STAT3             1773       3286       4547       2569       1089       2788
## SOST                 4          1         28          0          0         30
## ITGA2B               5          8          2          3          3          0
## EFCAB13             16         49          5         31         22          9
## NPEPPS             577       1015       1049        765        679        742
## TBX21                2          5          7          8         11          3
## COL1A1            5839      23680      14109      26893       6080       3426
## MRPS23             863        821        670        411        439        743
## MIR21                1          0          0          0          0          0
## RPS6KB1            230        487        323        403        219        346
## ACE                 33        195        144        271         44         60
## ERN1                82        222        222        150        111        126
## PRTN3                0          0          0          0          0          0
## PLIN5               72        470        176         30        237        168
## RETN                 1          5          1          2          0          0
## CCL25                0          0          0          2          0          0
## ICAM1              193        216        241        263        135        155
## TYK2               112        461        294        314        219        186
## SMARCA4            146        956        958        788        453        516
## ACP5               543        796       1097        483        615        934
## JUNB               728       1260       3615       1157        616       3150
## CYP4F22            533        881       1414        492        761        997
## JAK3                30         45         93         38         19         54
## JUND               682       1150       1319       1544        504        574
## CEBPA             1261       2633       4526       2275       1854       3347
## CEBPG              802       1128       1052        871        646       1043
## ACP7               390        168       1772        108        141       1552
## ZFP36              151        402        637        421        247        664
## TGFB1              283        603        950        883        283        334
## RPS19            19385      27659      22703      15531      16349      18502
## PSG2                 0          0          4          1          0          0
## FUT2               151         81        156         17          6         90
## NKG7                56          9         75         56         13         50
## ZNF415              43        204         30         36         61         18
## LILRB2              30         50         61         84         24         55
## LILRA5              20          2          8          2          0          3
## KIR3DL1              0          0          0          2          0          0
## KIR3DL2              0          0          1          0          0          1
## SMOX               298        215        796        158        200        393
## BMP2                89        133        160        262         83         76
## GINS1               96        101        136         66         71        185
## PLCG1              257        726        585        515        296        439
## YWHAB             2715       6265       5250       4921       3487       4007
## PI3              21003        128      22066         19         33      46097
## MMP9                20         55        209        104         59        172
## CD40               111        204        216        206        138        220
## PFDN4              392        407        297        233        387        434
## BMP7               101        443        645        579        234        255
## RPS21            15655      15485      10991       7946      11660      13162
## MX1                118        264        733        452        111       1715
## PFKL               492       2361       2073       1852        976        774
## IL17RA              87        413        239        283        192        193
## UBE2L3            1124       1685       1730       1079        954       1301
## TPST2              298        317        395        300        144        273
## XBP1              3759       3903       2838       1563       1463       2016
## UQCR10             867       1262       1054        568        649        885
## SEC14L2            101        261        210         96         90        200
## APOL6              317        337        495        395        213        884
## APOL1              231        159        297        200         97        495
## TYMP              1875       1060       4880        616        395       3238
## BEND2                0          0          0          0          0          0
## PHEX                10         26         22         35         20         41
## TIMP1              549       1171        863       1050        654        294
## FOXP3               15         49         41         22         31         60
## MSN               1979       3899       4386       4607       1732       2392
## PGK1              9838       7944      10089       4380       4144       7456
## LAMP2             2040       3983       2279       2303       2252       2337
## CD40LG               5         13         24         21         17         26
## IRAK1              529       1430       1918       1176        651        994
## COX2              4773      23140      10454      13710      12162       7377
##             GSM5630032 GSM5630033 GSM5630034 GSM5630035 GSM5630036
## TNFRSF9             13          4         36         37          6
## ENO1             13706       7619      19502      19107       2925
## PIK3CD             172        105        209        465         68
## PGD               3314       1118       2324       5151        502
## MTHFR              370        183        380        930        119
## TNFRSF1B           371        207       1013        991         93
## PINK1             2109       1170       1547       3526        509
## IFNLR1             154         55        109        368         26
## RUNX3              482        344        461       1441         96
## SH3BGRL3          3025       1908       4416       3649       1034
## CD52               256        111        383       1160        444
## IFI6               630        965       1848       1002        483
## ZC3H12A            728        108       1203        914         60
## UTP11              676        424        796       1227        475
## JUN                776        487       1128       3238        212
## KANK4               41         10         18        136          1
## EFCAB7             107         53        102        315        105
## IL23R                0          0          4          3          3
## ADGRL2             568        216        522       1408        130
## GBP3               414        269        402        478        314
## GBP1               325        222       1061        679        150
## GBP5                60         43        195        167         47
## TGFBR3            1201        682       1131       3095        388
## VCAM1              330        120        527        681        164
## PTPN22              28         31         77        123         24
## CD160                8          3         23         20          3
## FCGR1A               6          3        213         16         16
## MCL1              3067       2123       4141       6855       1073
## CTSK             12583       9343      13370      20138       9129
## RORC               713        326        182       1461        119
## S100A9            2797        245     183809       8612        103
## S100A12              6          0       1028          5          0
## S100A8            2567        200     138251       9031        103
## IL6R               366        294        459        817        119
## RIT1               469        272        620        961        261
## BGLAP               17         11         13         17          8
## IFI16             1762        817       2538       3060        482
## AIM2                10          4         49         41         11
## CRP                  0          0          0          0          0
## FCGR2A             107         91        443        236         52
## HSPA6               82         59        237        161         21
## FCGR3A              33         39        603         77         26
## SELL                26         25        161         81         14
## GLUL              8541       5475      12587      12226       3051
## PTGS2               16         23        110        107         20
## CRB1                 8          1          5          3          5
## KDM5B             1410        519        941       2980        306
## IL10                 5         10         22         38         11
## YOD1               612       1000       1746       1440        379
## HHAT               141         45         90        291         31
## TRAF5               87         80        194        291         59
## NLRP3               16         17         79         66          9
## LINC01250            0          0          0          0          0
## RPS7             36522      19857      21978     140215      44088
## RSAD2               52         53        155        101         47
## FOSL2             2654       1615       2601       7737        393
## REL                487        203        709       1550        165
## TGFA               830        440       1075       1378        297
## DYSF               192        105        394        405         37
## HK2                783        192       1240       2067         76
## CD8A               153         22        189        105         83
## CD8B                87         21         57         54        122
## EIF5B             2584       1664       2962       5342        796
## IL1R1             1319        795       2201       3376        535
## RGPD6              239        130        177        506         79
## IL1A                70         32         21        175         42
## IL1B                30          0        144         63          5
## IL37              1147        855        458       1211        596
## IL36RN            1498       1267       6207       2014        675
## IL1F10              83         94         80        126         61
## IL1RN             1824       1004       1781       1945        465
## NMI                580        306        815        770        403
## TNFAIP6             76         54        105         47         72
## IFIH1              351        193        353        742        102
## SCN1A                3          3          1         17          0
## ABCB11              36          6          5        104          8
## RBM45               95         64        117        170         32
## FRZB               150        250        675       1529        141
## TFPI               511        289        525        603        445
## STAT1             1649       1151       3515       3069        477
## NABP1              148         45        307        324         36
## SF3B1             3201       1794       3343       7068       1152
## CASP10             143         84        242        364         79
## CD28                52         12        135        127         33
## CTLA4                5          1         37         41          3
## ICOS                17          4         45         43          9
## NDUFS1            2486        930       1843       4449        615
## CXCR2              122         27        258        171         13
## IRS1               376        244        285       1264         80
## CCL20               13          0         34         33          7
## ATG16L1            375        262        490       1248        130
## GPR35               17          8         23         30          1
## PDCD1               12          7         25         18          4
## PPARG              619         91        245       1062        113
## RPL15            54743      31341      33670      91904      43168
## EOMES               12          3         31         19         14
## CX3CR1              96         57        206        247         32
## ACKR2                7         12         71         62          6
## CCR2               151        110        271        316        135
## CCRL2               10          8         45         16          6
## TLR9                 3          4         10         14          0
## ARHGEF3            542        301        794       1006        225
## ADAMTS9             58         54        224        356         17
## TMEM45A          15806       5708      12071      21020       5402
## CD80                 1          1         21         14          0
## CD86               127         66        235        288        150
## MIX23              249        144        188        474        202
## PLS1                73         58         86        244         23
## PTX3                29         11        215         65         17
## GOLIM4             633        446       1018       2279        246
## MYNN               546        339        516       1340        489
## TNFSF10           2090        737       2098       3900       1429
## ADIPOQ             263         21       1002         74          9
## SPON2              624        623        626        883        103
## S100P              318         77        683       1243         98
## WDR1              4182       2629       6203       7072        819
## CD38                 5          3         21         10          4
## PPARGC1A           173         92        142        869         69
## TMPRSS11B            0          0          0          0          0
## CSN3                 0          0          0          2          0
## ALB                  6          0          4          5          0
## CXCL8                2          0       3140         20          1
## CXCL2                5          1         31         12          4
## AREG                68         15         77        195         17
## CXCL10              14          1        149         89         17
## CXCL13               7          1        137         31          4
## SPP1                 6          7         22        398          4
## HERC6              121         87        267        314         40
## NFKB1              848        498       1025       2355        206
## SEC24B             648        315        507       1545        182
## EGF                 23         25         19        175          4
## IL2                  4          0          0         16          5
## IL21                 0          0          2          0          0
## IL21-AS1             0          0          1          0          0
## SLC7A11             18          9        105         57         10
## IL15                61         47         95        163         77
## EDNRA              183        140        375        558         61
## TLR2               227         48        197        391         53
## FGB                  0          0          0          0          0
## DDX60              443        426        446       1026        139
## SPCS3             1802       1245       2607       3711       1234
## TLR3               115         42        114        220         51
## OSMR               348        157        706        972         70
## GZMK                59         19         76         72         99
## GZMA                59         21        123        110        166
## ANKRD55              7          2          4          8          2
## CENPK               81         59         71        170         69
## CAST              5627       3857       5856      10306       1745
## ERAP1             1442        969       1395       3722        437
## ERAP2             1165        291        725       1351        213
## TNFAIP8            903        535       1007       1386        866
## CSF2                 0          0          0         13          2
## IL5                  2          0          0          0          0
## IL13                 0          0          2          5          0
## IL4                  1          1          1          1          1
## CD14               608        824       2236        910        267
## CSNK1A1           5554       3661       7705       9079       1639
## PPARGC1B           143         48        159        586         31
## TNIP1             2284       1093       2892       3567        453
## ATOX1              672        405        761       1021        403
## FAXDC2            1736        376        503       5274        175
## IL12B                0          0          4          8          0
## MIR146A              1          0          2          1          0
## PDLIM7             371        237        819        773         62
## SERPINB1           717        614       1351       1271        655
## SSR1              2220       1215       2499       4125        716
## CD83                83         44        238        273         70
## SOX4               600        341        655       2115        203
## CMAHP              188        189        226        569        194
## HLA-A            22716      12097      20862      26458       5940
## HLA-C            28740       9011      21219      22880       6588
## HLA-B            32612      15618      31069      32799       9737
## MICA               208        165        273        725        159
## LTA                 11          1         12         34          5
## TNF                 24          8         49        149         15
## HLA-DRB1          7685       3549       5694       4544       2750
## HLA-DQB1          1090       1041        903        872        308
## PPARD              792        518       1685       1940        125
## CCND3             1027        650       1268       1703        301
## VEGFA              602        235        505       1279        142
## RUNX2               26         30         74        202         13
## IL17A                0          0          5          0          0
## IL17F                0          0          6          0          0
## PRDM1              349        268       1044       1105        132
## ATG5               680        390        703       1357        559
## TRAF3IP2           799        486        722       1372        137
## NCOA7              530        234        616       1057        197
## SGK1               970        723       1992       2440        344
## IFNGR1            1971       1220       2589       4390       1727
## TNFAIP3            275        128        369       1100        114
## SOD2              4369       2168      13578       8915       1594
## LPAL2                3          0          2          5          0
## PLG                  0          3          1          2          1
## CCR6                64         53        103        293         59
## RAC1              5715       3813       5746       7562       1855
## ZNF316             522        343        461       1442        148
## AHR               1605        855       2262       4237        551
## IL6                  0          1          3          2          1
## TOMM7             4636       3366       2950       7048       3704
## CYCS              3385       1652       4187       6232       1832
## AQP1              6444       4819       8033       8595       2061
## NT5C3A             853        598       2250       1449        592
## EGFR              2556       1329       1595       8413        538
## CD36              2051        970       4152       5255        385
## SAMD9              109         59        330        427         38
## SERPINE1            45         52        255         73         27
## CUX1               847        592       1220       2065        173
## PSMC2             2681       1806       2960       3744       1269
## NAMPT             2419       1392       4090       3831       1023
## HYAL4               12          4         85         29          1
## LEP                 52         11        285         24          3
## CALD1             4120       3015       9375       7847       1166
## BRAF               365        216        365       1023        127
## EZH2               234        165        280        499        106
## DNAJB6            3884       2203       5031       5652       1443
## CSMD1               37          9         19        101          0
## CTSB              8572       5160      17808      18238       1923
## EGR3              1049        542        717       2508        159
## TNFRSF10A          104         49        103        240         20
## BNIP3L            5004       2173       4022       6953       2022
## DUSP4              535        180        350       1810         73
## NRG1                75         48        101        188         34
## RPL7             78092      42079      46472      95916      56925
## IL7                169        126        133        271        153
## GEM                145         98        509        334         73
## MYC                775        549        964       2164        169
## GPT               1656        274        150       2022        112
## JAK2               488        270        604       1133        200
## CD274               15         12         77         82         16
## IL33              1937        806       1047       1903       1646
## LURAP1L-AS1          7          1          1          7          2
## LURAP1L            226        250        473        682        144
## TTC39B            1973        469        917       3245        550
## IFNA1                0          0          0          0          0
## TEK                166        116        272        270         40
## TRBV20OR9-2          0          0          0          0          0
## TOMM5             1236        758       1352       3434       1209
## ANXA1             6776       4775      12695       9859       5955
## ERP44              947        538       1054       1539        408
## ZNF483              67         30         54        154         27
## TNFSF15             26          4         22         83          4
## TLR4               232        331        648        524        354
## PTGS1             2756       2281       1995       5260        870
## HSPA5             6225       3267       8034      13999       1457
## FNBP1              987        738       1288       2358        373
## CARD9               91         35        111        253         10
## TRAF2              283        132        263        640         44
## CLIC3             1448       1405       1467       1527        284
## IL2RA               15         10         68         54          7
## GATA3             2697       1706        822       5751        661
## VIM              25899      20078      34119      33058       9436
## CREM               328        199        374        680        231
## DKK1                21         52         37         32          7
## MBL2                 0          0          1          1          0
## SAR1A             1777       1011       1969       3490        902
## PRF1                44         16        107         61         18
## ZMIZ1              965        571       1203       4053        161
## IFIT3              361        329        690        607        299
## TALDO1            4807       2189       3156       5591       1427
## IGF2               269        133        595        323         98
## INS-IGF2           262        121        563        299         95
## IGF2-AS              1          0          0          0          0
## INS                  0          0          0          0          0
## STIM1             1305        720       1224       3190        234
## TRIM22             692        666       1089       1539        432
## PTH                  0          0          0          0          0
## SAA1               619         33        766       1433        131
## SLC1A2             100         15         32        111         14
## FOSL1                2         19         84         14          0
## CCND1             4079       2294       2376      10044        749
## JRKL               153         73        110        472         25
## MMP7               466        220        320       1287         89
## MMP1                12          0         37        135          3
## MMP3                 2         18         13         15          0
## CASP1              862        591       1089       1724        596
## DLAT               784        426        751       1480        171
## IL18              2691       2690       1701       4209       2863
## CD3E               199         48        254        323         92
## MCAM              1620        561       5087       2393        336
## WNK1              2856       1868       2929       9442        729
## TNFRSF1A          3205       1837       2690       3939        569
## GAPDH            22467      16159      29623      29843       6821
## CD4                672        532       1059       1590        299
## SLC2A3             185        103        357        361         68
## CLEC4D               3          0         17          4          0
## KLRB1               45         26         90         96         39
## CD69                55         17         52        215        136
## CLEC2B            1844       1269       1750       4359       2813
## OLR1                 1          0          6         11          0
## ABCD2               12          7         42         55         13
## LRRK2              176        175        192        449        105
## VDR                779        300        597       3121        107
## TMBIM6           18799       7515      10465      24582       4585
## PFDN5             8505       4610       6012      39189      10917
## SP7                  1          0          1          2          0
## MUCL1              164        387       2983       5242         36
## CD63             12408      10463      15232      21435      11957
## SUOX              1936        920       1315       3318        360
## RPS26             5267      12099       4636      12763       3339
## RPL41           106256      57211      61002     315059     111396
## IL23A                1          2          9         19          1
## DDIT3              303        127        220        625        162
## IFNG                 0          1          3          2          0
## IL22                 0          0          0          0          0
## LYZ               2200       1196       9034       6003       3225
## CAPS2               53         33         42        125         27
## SYT1                 8         11         25         61         15
## BTG1              6365       2980       5203       9067       2908
## HCAR3              182        111        421        402         82
## GJB2              1654        610       8537       4836        173
## GJB6               976        547       5002       3034        378
## TNFSF11              5          1          8         29          7
## TPT1            146293      83460     123801     417950     177950
## LMO7               576        343       1134       1653        161
## TNFSF13B           160        112        371        221        166
## LAMP1             5175       2598       3438       8993        612
## PSME2             1241        724       2398       2177        787
## GZMB                 0          8        138         24         14
## RPL36AL           5455       2497       4109       7793       3235
## PYGL              1096        480       1697       1583        220
## HIF1A              811        500       1591       2826        222
## FOS                329        178        355      13831       1032
## JDP2               811        676        698       1090        327
## NOXRED1             10          4         13         22          0
## SERPINA1            47         20        534        238         35
## CDC42BPB          1240        908       1600       3950        259
## PLA2G4D            269         79       2270        580         50
## TRIM69               9          6         16         25          7
## SLC51B              27          8         63         27          9
## SMAD3              815        429        690       1620        251
## CYP1A1              22        184          1         12          3
## AKAP13            1299        837       1679       4769        428
## MEFV                 6          4         38         15          5
## SOCS1               70         77         79        136         35
## ATXN2L             737        367        618       2038        149
## CD19                 0          0          5          5          0
## ITGAL               75         20        137        272         39
## ITGAM              150        175        219        423         76
## ITGAX               42         23        146        218         24
## DNAJA2            2084       1317       2219       3254       1016
## SIAH1              414        259        451        738        241
## ADCY7              551        409        703       1975        173
## NOD2               222        102        431        674         63
## CMTM2                4          0         14          8          2
## SF3B3             2054       1048       1656       4358        328
## PSMD7             2523       1523       2602       3612       1128
## WWOX                96         67        331        288         46
## MAF               2556       1598       2277       6300        645
## SLC7A5             893        626        965       2056         67
## CXCL16             582        269        777       1142        113
## XAF1               263        156        356        512        115
## CD68               797        895       1887       1436        337
## PER1              1225        806       1191       2108        394
## NOS2                 0          8         21          4          3
## TRAF4              538        255        486       1053        199
## CCL2               254         64        236        491        214
## CCL5               229         29        270        173        107
## CCL3                 3          4         66         21          2
## CCR7                22         14        160        113         23
## STAT3             3321       1614       5818       9402        608
## SOST                 0          9         48          7          0
## ITGA2B              28          7          6         14          6
## EFCAB13             34         21         28         88         11
## NPEPPS            1265        737       1179       2811        309
## TBX21               18          2         16         16          0
## COL1A1           31968       9072      54374     129728      11321
## MRPS23             833        496        910       2156        683
## MIR21                0          1          5          1          0
## RPS6KB1            533        299        698       1283        177
## ACE                185         99        300        469         34
## ERN1               286        115        316        984         92
## PRTN3                0          0          3          0          0
## PLIN5             1060         65        126       1637         72
## RETN                 2          0         26          6          1
## CCL25                0          1          0          0          0
## ICAM1              208        138        427        616         99
## TYK2               636        349        646       1578        178
## SMARCA4           1243        670       1219       3952        216
## ACP5              1315        589       1411       1624        326
## JUNB              2528       1413       2912       5495        483
## CYP4F22           1675        617       1682       3040        152
## JAK3                40         23        154        158         24
## JUND              1678       1637       1498       2258        391
## CEBPA             5595       3001       3963       6858        933
## CEBPG             1333        868       1355       2259        581
## ACP7               145        160       1630        703         46
## ZFP36              586        347        975       1961        217
## TGFB1              962        783       1531       1606        232
## RPS19            38949      26146      26689      69794      30625
## PSG2                 2          0          0          1          1
## FUT2                40         38        133        220         14
## NKG7                57         25        143         27         26
## ZNF415             183         44         63        265         64
## LILRB2              44         35        287        116         27
## LILRA5               1          4         78         10          6
## KIR3DL1              0          0          0          1          0
## KIR3DL2              0          0          0          5          2
## SMOX               223        263        570        488         35
## BMP2               239        186        247        457        111
## GINS1              150        109        159        222        104
## PLCG1              730        438        918       2468        185
## YWHAB             6650       4301       7098       9943       2251
## PI3                332         53      16297        249         12
## MMP9                92         52        549        797         32
## CD40               395        235        338        499        166
## PFDN4              536        365        427       1265        703
## BMP7               681        460        749       1301         98
## RPS21            23107      12946      13244     102479      27670
## MX1                216        233        571        543         95
## PFKL              3080       1697       2664       6563        490
## IL17RA             515        258        627       1468         91
## UBE2L3            1999       1200       2098       3027        732
## TPST2              522        353        573        867        139
## XBP1              4194       1879       4334       7318       1276
## UQCR10            1822        746       1196       3013        921
## SEC14L2            187         66        306        558         48
## APOL6              402        205        991       1052        181
## APOL1              177        115        638        544         66
## TYMP              1373        705       5913       2483        251
## BEND2                0          0          0          3          2
## PHEX                18         19         31         49         15
## TIMP1             1298       1076       2099       1784        578
## FOXP3               58         33         98        158          7
## MSN               4161       3343       9148       8540       1130
## PGK1              8534       5477      11473      14256       4439
## LAMP2             4790       2275       3242       7064       1796
## CD40LG              35          2         39         78         22
## IRAK1             1784       1316       2605       3550        420
## COX2             34537      16093      16953      65836      11496

4. Selection of samples

Selection of samples related to psoriatic arthritis and ankylosing spondylitis from the dataset

# sample selection
gsms <- "XX2210102XX2102XX21021010200101010XXXXXXXX10XXXXXX10XX10102XX2XX2"
sml <- strsplit(gsms, split="")[[1]]

# Filter out excluded samples (marked as "X")
sel <- which(sml != "X")
sml <- sml[sel]
expr_data <- expr_data_filtered[, sel]

# group membership for samples
gs <- factor(sml)
groups <- make.names(c("non lesion PsA", "lesion PsA", "normal skin AS"))
levels(gs) <- groups
sample_info <- data.frame(Group = gs, row.names = colnames(expr_data))


dsa <- DESeqDataSetFromMatrix(countData=expr_data, colData=sample_info, design= ~Group)
dsb <- DESeq(dsa, test="LRT", reduced = ~ 1)  # Use LRT for all-around gene ranking
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
# extract results for top genes table
r <- results(dsb, alpha=0.05, pAdjustMethod ="fdr")

plotDispEsts(dsb, main="GSE186063 Dispersion Estimates")

# create histogram plot of p-values
hist(r$padj, breaks=seq(0, 1, length = 21), col = "grey", border = "white",
     xlab = "", ylab = "", main = "GSE186063 Frequencies of padj-values")

#After filtering which groups have some expressed genes
cts <- list(c("Group",groups[1],groups[2]),
            c("Group",groups[3],groups[2]),
            c("Group",groups[1],groups[3]))  # contrasts of interest


# Wald test to obtain contrast-specific results
dsc <- DESeq(dsa, test = "Wald", sfType = "poscount")
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
r <- results (dsc, contrast=cts[[1]], alpha=0.05, pAdjustMethod = "fdr")


# Venn diagram
library(gplots)
all_res <- list()

for (ct in cts) {
  i <- length(all_res)
  r <- results(dsc, contrast=ct, alpha=0.05, pAdjustMethod = "fdr")
  all_res[[i + 1]] <- rownames(r)[!is.na(r$padj) & r$padj < 0.05 & abs(r$log2FoldChange) >= 1.0 ]
  names(all_res)[i + 1] <- paste(ct, collapse="_")
}
venn(all_res)

5. Differential gene expression analysis

# Differential gene expression analysis
df <- as.data.frame(r)
df <- na.omit(df)

topGenes <- rownames(df)
heatmapData <- expr_data[topGenes, ]

# Load the necessary libraries
library(pheatmap)
library(RColorBrewer)

# Calculate the average expression for each gene
media_dos_genes <- rowMeans(heatmapData)

# Sort the averages in descending order
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)

# Get the names of the first 20 genes
top_20_genes_por_media <- names(head(media_ordenada, 20))

# Filter the original matrix to retain only the 20 selected genes
heatmapData_top20 <- heatmapData[top_20_genes_por_media, ]

# Create column annotation with groups
annotation_data <- data.frame(
  group = sample_info$Group,
  row.names = rownames(sample_info)
)

# Reorder columns by group
ordem_grupo <- order(annotation_data$group)  # Ordena por nome do grupo (alfabética)
heatmapData_top20 <- heatmapData_top20[, ordem_grupo]
annotation_data <- annotation_data[ordem_grupo, , drop = FALSE]

# Read the libraries below
library(ComplexHeatmap)
library(circlize)

# Matrix of the 20 genes
mat <- heatmapData_top20

# Reschedule by line
mat_scaled <- t(scale(t(mat)))

# Create group annotation
ha_col <- HeatmapAnnotation(
  Group = annotation_data$group,
  col = list(Group = c("lesion.PsA" = "#d62728",
                       "non.lesion.PsA" = "#1f77b4",
                       "normal.skin.AS" = "green"))
)

# Inverted RdBu colour palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))

# Heatmap with clustering within groups
Heatmap(
  mat_scaled,
  name = "Z-score",
  top_annotation = ha_col,
  col = cores,
  cluster_columns = TRUE,              
  cluster_column_slices = TRUE,       # << cluster within each group
  column_split = annotation_data$group, # << separate the columns by group
  cluster_rows = TRUE,
  show_column_names = FALSE,
  show_row_names = TRUE,
  column_title = "Heatmap of the 20 most highly expressed genes (average) from GSE186063",
  heatmap_legend_param = list(title = "Z-score")
)

# UMAP plot (multi-dimensional scaling)
expr_data_umap <- expr_data[rowSums(expr_data) > 0, ] # Remove rows with zero sum
u <- umap(t(expr_data_umap), n_neighbors=15, random_state=123)

plot(u$layout, main="GSE186063 UMAP", xlab="", ylab="", tcl=0.1, pch=19, col="blue")
text(u$layout, labels=colnames(expr_data_umap), cex=0.7, pos=3)

# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(df)

# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)
## 'select()' returned 1:1 mapping between keys and columns
# First, convert the rownames from df into a column
df$Symbol <- rownames(df)

# Join the original table and the converted IDs
dfd <- merge(df, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)

# Ensure unique symbols
dfd <- dfd[!duplicated(dfd$ENTREZID), ]

6. Comparison between skin samples from non-lesions of psoriatic arthritis versus lesions of psoriatic arthritis

# Wald test to obtain contrast-specific results
dsd <- DESeq(dsa, test = "Wald", sfType = "poscount")
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
r <- results(dsd, contrast = c("Group", groups[1], groups[2]), alpha = 0.05, pAdjustMethod = "fdr")


# Filter only significant genes
sig_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) >= 1)


# volcano plot
old.pal <- palette(c("#00BFFF", "#FF3030")) # low-hi colors
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log2FoldChange, -log10(padj), main=paste(groups[1], "vs", groups[2]),
       xlab="log2FC", ylab="-log10(Padj)", pch=20, cex=0.5)
  text(log2FoldChange, -log10(padj), labels=rownames(r), cex=0.6, pos=4)
})
with(subset(r, padj<0.05 & abs(log2FoldChange) >= 1),
     points(log2FoldChange, -log10(padj), pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1))
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20,col=1:2)

# Plot only significant genes
#MD PLOT
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log10(baseMean), log2FoldChange,
       main=paste(groups[1], "vs", groups[2]),
       xlab="log10(mean of normalized counts)", ylab="log2FoldChange",
       pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1)
  text(log10(baseMean), log2FoldChange, labels=rownames(sig_genes), cex=0.6, pos=4)
})
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20, col=1:2)
abline(h=0)

palette(old.pal) # restaurar paleta

# Add the gene symbols to the points on the graph.

library(ggplot2)
library(ggrepel)

plotVolcano <- function(res, title = "Volcano Plot") {
  res$group <- "NS"
  res$group[res$padj < 0.05 & res$log2FoldChange > 1] <- "Up"
  res$group[res$padj < 0.05 & res$log2FoldChange < -1] <- "Down"
  
  res$label <- ifelse(res$group != "NS", rownames(res), NA)
  
  ggplot(res, aes(x = log2FoldChange, y = -log10(padj), color = group)) +
    geom_point(alpha = 0.7, size = 2) +
    geom_hline(yintercept = -log10(0.05), linetype = "dashed") +
    geom_vline(xintercept = c(-1, 1), linetype = "dashed") +
    scale_color_manual(values = c("Up" = "firebrick", "Down" = "dodgerblue", "NS" = "grey80")) +
    ggrepel::geom_text_repel(aes(label = label), size = 3, max.overlaps = Inf) +
    theme_minimal() +
    labs(title = title, x = "log2 Fold Change", y = "-log10 adjusted p-value", color = "Regulation")
}

# Example of function usage
plotVolcano(r, paste(groups[1], "vs", groups[2]))
## Warning: Removed 4 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 308 rows containing missing values or values outside the scale range
## (`geom_text_repel()`).

# Genes upregulated
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange >= 1))

# Genes downregulated
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange <= -1))

# All DEGs with |log2FC| > 2
de_genes <- c(up_genes, down_genes)

# Display gene symbols before conversion
expr_datasa <- as.data.frame(expr_data[rownames(expr_data) %in% de_genes, ])

# Convert expression data to long format for ggplot2
expr_datas <- as.data.frame(expr_datasa)
expr_datas$Gene <- rownames(expr_datas)
expr_datas <- pivot_longer(expr_datas, cols = -Gene, names_to = "Sample", values_to = "Expression")
expr_datas <- merge(expr_datas, pheno_data, by.x = "Sample", by.y = "geo_accession")

# Check column names and a sample of the data
expresse <- r[order(r$padj)[1:429], ]
expresse <- merge(as.data.frame(expresse), expr_datasa, by = 0, sort = F)


library(dplyr)
library(tibble)
library(clusterProfiler)
library(ggplot2)

r_df <- as.data.frame(r)

# This ensures that gene names are preserved
r_df_com_genes <- r_df %>%
  rownames_to_column(var = "Gene") 

# --- Now, the rest of your code works perfectly ---
top30_fc <- r_df_com_genes %>%
  # O 'filter' também pode ser conflitante, é bom usar o prefixo
  dplyr::filter(padj < 0.05 & abs(log2FoldChange) > 1) %>%
  dplyr::arrange(desc(abs(log2FoldChange))) %>%
  # Esta é a correção principal:
  dplyr::slice(1:30) %>%
  dplyr::mutate(
    Regulation = case_when(
      log2FoldChange > 1 ~ "Upregulated",
      log2FoldChange < -1 ~ "Downregulated"
    )
  )


# Graph with positive and negative bars (your code here is perfect)
ggplot(top30_fc, aes(x = reorder(Gene, log2FoldChange), y = log2FoldChange, fill = Regulation)) +
  geom_col() +
  coord_flip() + # Coloca os genes no eixo Y
  scale_fill_manual(values = c("Upregulated" = "steelblue", "Downregulated" = "tomato")) +
  scale_y_continuous(breaks = seq(-8, 4, by = 1)) + # Ajuste os limites se necessário
  theme_bw() +
  labs(
    title = "The 30 most prominent DEGs between non-lesion and lesion PsA (GSE186063)",
    x = "Gene",
    y = "log2 Fold Change",
    fill = "Regulation"
  ) + 
  theme(
    axis.text.y = element_text(color = "black", face = "bold", size = 9)
  )

# --- Select the 20 MOST overexpressed genes (Your code here is perfect) ---
up_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange > 1) %>%
  arrange(desc(log2FoldChange)) %>% 
  head(20) %>%
  pull(Row.names)

# --- Filters expression data ---
expr_datas_filtrado_up <- expr_datas %>%
  filter(`diagnosis:ch1` == "Psoriatic Arthritis") %>%
  filter(`source_name_ch1` %in% c("non-lesion", "lesion")) %>% 
  filter(Gene %in% up_20genes)

# --- Calculate the average per gene and per group ---
expr_datasa_up <- expr_datas_filtrado_up %>%
  group_by(Gene, `source_name_ch1`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    sd_expression = sd(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---
dados_para_plotar_up <- expr_datasa_up %>%
  filter(source_name_ch1 == "non-lesion")

# --- Graph Generation ---
ggplot(dados_para_plotar_up, aes(x = mean_expression, y = reorder(Gene, mean_expression))) +
  geom_col(fill = "steelblue", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Upregulated Genes in Non-Lesion Skin", # Título mais claro
    subtitle = "For non-lesion PsA vs lesion PsA (GSE186063)",
    x = "Average Expression in the Group 'Non-Lesion'", # Rótulo do eixo mais claro
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- Selects the 20 MOST under-expressed genes ---
down_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange < -1) %>%
  arrange(log2FoldChange) %>% # <-- Sort from most negative to least negative
  head(20) %>%
  pull(Row.names)

# --- Filters expression data for genes and groups of interest ---
expr_datas_filtrado_down <- expr_datas %>%
  filter(`diagnosis:ch1` == "Psoriatic Arthritis") %>%
  filter(`source_name_ch1` %in% c("lesion", "non-lesion")) %>%
  filter(Gene %in% down_20genes)

# --- Calculate the average per gene and per group ---
expr_datasa_down <- expr_datas_filtrado_down %>%
  group_by(Gene, `source_name_ch1`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---'
dados_para_plotar <- expr_datasa_down %>%
  filter(source_name_ch1 == "non-lesion")

# --- Graph Generation ---
ggplot(dados_para_plotar, aes(x = mean_expression, y = reorder(Gene, -mean_expression))) +
  geom_col(fill = "red", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Downregulated Genes in Non-Lesion Skin", # Título mais claro
    subtitle = "For non-lesion PsA vs lesion PsA (GSE186063)",
    x = "Average Expression in the Group 'Non-Lesion'", # Rótulo do eixo mais claro
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- Create 'count_matrix' ---
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange > 1))
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange < -1))
genes_interesse <- c(up_genes, down_genes)

expr_filtrado <- expr_datas %>%
  filter(`diagnosis:ch1` == "Psoriatic Arthritis") %>%
  filter(`source_name_ch1` %in% c("non-lesion", "lesion")) %>%
  filter(Gene %in% genes_interesse)

matriz_contagem <- expr_filtrado %>%
  select(Gene, Sample, Expression) %>%
  pivot_wider(names_from = Sample, values_from = Expression, values_fill = 0) %>%
  column_to_rownames(var = "Gene")


# Filter your original “sample_info” object to keep only the samples that are in your final matrix.
# This ensures that the annotation corresponds exactly to the heatmap data.
sample_info_filtrado <- subset(sample_info, rownames(sample_info) %in% colnames(matriz_contagem))


# Select the 20 most highly expressed genes 
media_dos_genes <- rowMeans(matriz_contagem)
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)
top_20_genes_por_media <- names(head(media_ordenada, 20))
heatmapData_top20 <- as.matrix(matriz_contagem[top_20_genes_por_media, ])


# Create the annotation for the heatmap from the already filtered information.
annotation_data <- data.frame(
  Group = sample_info_filtrado$Group,
  row.names = rownames(sample_info_filtrado)
)

# Ensure that the order of the columns in the heatmap and annotation is the same.
heatmapData_top20 <- heatmapData_top20[, rownames(annotation_data)]


# --- Heatmap generation with ComplexHeatmap ---

library(ComplexHeatmap)
library(circlize)
library(RColorBrewer)

# Rescale data by row (Z-score)
mat_scaled <- t(scale(t(heatmapData_top20)))

# Create the column annotation
ha_col <- HeatmapAnnotation(
  Group = annotation_data$Group,
  col = list(Group = c("non.lesion.PsA" = "#1f77b4", "lesion.PsA" = "#d62728"))
)

# Define the colour palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))

# Generate the heatmap
Heatmap(
  mat_scaled,
  name = "Z-score",
  top_annotation = ha_col,
  col = cores,
  
  # Divide the columns into groups for clearer viewing
  column_split = annotation_data$Group,
  
  cluster_rows = TRUE,
  cluster_columns = TRUE, # Cluster within each divided group
  
  show_column_names = FALSE,
  show_row_names = TRUE,
  column_title = "Heatmap of the 20 most highly expressed DEGs (non-lesion vs. lesion PsA GSE186063)",
  heatmap_legend_param = list(title = "Z-score")
)

# Filter differentially expressed genes
de_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) > 1)

# Create a data frame from de_genes
de_genes <- data.frame(de_genes)

# Suppose your dataframe is called df and you want to select columns ‘column1’, “column2” and ‘column3’.
de_genes <- de_genes %>% select(log2FoldChange, padj)

# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(de_genes)

# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)
## 'select()' returned 1:1 mapping between keys and columns
# First, convert the rownames from df into a column
de_genes$Symbol <- rownames(de_genes)

# Join the original table and the converted IDs
de_genes <- merge(de_genes, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)

# Ensure unique symbols
de_genes <- de_genes[!duplicated(de_genes$ENTREZID), ]

# View the first results to verify the addition of the IDs
de_genes <- de_genes %>% 
  filter(Symbol %in% rownames(matriz_contagem))
                               

BiocManager::install("GOSemSim")
## 'getOption("repos")' replaces Bioconductor standard repositories, see
## 'help("repositories", package = "BiocManager")' for details.
## Replacement repositories:
##     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
## Bioconductor version 3.20 (BiocManager 1.30.26), R 4.4.1 (2024-06-14)
## Installing package(s) 'GOSemSim'
## Warning in install.packages(...): installation of package 'GOSemSim' had
## non-zero exit status
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##   path: /usr/local/lib/R/library
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##     boot, class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv,
##     nlme, nnet, rpart, spatial, survival
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##     annotate, AnnotationDbi, ape, aplot, askpass, BH, Biobase, BiocFileCache,
##     BiocGenerics, BiocManager, BiocParallel, BiocVersion, biomaRt, Biostrings,
##     bit, bit64, bitops, Boruta, broom, bslib, C50, car, caret, checkmate, chk,
##     classInt, cli, clock, clue, clusterProfiler, colorspace, commonmark,
##     ComplexHeatmap, corrplot, cowplot, cpp11, credentials, crosstalk, Cubist,
##     cutpointr, dbplyr, dbscan, DelayedArray, DEoptimR, Deriv, DESeq2, devtools,
##     DiceKriging, diffobj, doBy, docopt, DOSE, dotCall64, downloader, DT,
##     dtplyr, edgeR, enrichplot, entropy, evaluate, fastDummies, fastmatch,
##     fgsea, fitdistrplus, fontawesome, forcats, fs, future, future.apply,
##     gargle, GDCRNATools, genefilter, generics, GenomeInfoDb, GenomeInfoDbData,
##     GenomicDataCommons, GenomicRanges, gert, ggforce, ggfun, ggnewscale,
##     ggplot2, ggplotify, ggpubr, ggraph, ggridges, ggsci, ggtree, gh, gld,
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##     here, hms, httpuv, httr2, IRanges, jpeg, jsonlite, KEGGgraph, KEGGREST,
##     keras, KMsurv, knitr, labelled, later, lava, lavaan, lgr, limma, littler,
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##   'promises', 'reticulate', 'RSQLite', 'xfun'
library(GOSemSim)
  
BiocManager::install("enrichplot")
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## 'help("repositories", package = "BiocManager")' for details.
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##     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
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##     boot, class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv,
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##     BiocGenerics, BiocManager, BiocParallel, BiocVersion, biomaRt, Biostrings,
##     bit, bit64, bitops, Boruta, broom, bslib, C50, car, caret, checkmate, chk,
##     classInt, cli, clock, clue, clusterProfiler, colorspace, commonmark,
##     ComplexHeatmap, corrplot, cowplot, cpp11, credentials, crosstalk, Cubist,
##     cutpointr, dbplyr, dbscan, DelayedArray, DEoptimR, Deriv, DESeq2, devtools,
##     DiceKriging, diffobj, doBy, docopt, DOSE, dotCall64, downloader, DT,
##     dtplyr, edgeR, enrichplot, entropy, evaluate, fastDummies, fastmatch,
##     fgsea, fitdistrplus, fontawesome, forcats, fs, future, future.apply,
##     gargle, GDCRNATools, genefilter, generics, GenomeInfoDb, GenomeInfoDbData,
##     GenomicDataCommons, GenomicRanges, gert, ggforce, ggfun, ggnewscale,
##     ggplot2, ggplotify, ggpubr, ggraph, ggridges, ggsci, ggtree, gh, gld,
##     glmnet, globals, glue, GO.db, googledrive, googlesheets4, GOSemSim, gower,
##     GPArotation, gplots, graph, graphlayouts, gtable, hardhat, haven, HDO.db,
##     here, hms, httpuv, httr2, IRanges, jpeg, jsonlite, KEGGgraph, KEGGREST,
##     keras, KMsurv, knitr, labelled, later, lava, lavaan, lgr, limma, littler,
##     lme4, lmom, locfit, lubridate, magrittr, markdown, MatchIt, MatrixGenerics,
##     MatrixModels, matrixStats, maxstat, mice, mime, miniUI, mlbench, mlr3,
##     mlr3learners, mlr3measures, mlr3misc, mlr3pipelines, modeltools, multcomp,
##     mvtnorm, networkD3, nloptr, org.Hs.eg.db, party, partykit, patchwork,
##     pathview, pbapply, pbkrtest, pillar, pkgbuild, pkgdown, pkgload, plotly,
##     pROC, processx, prodlim, progressr, PRROC, ps, psych, purrr, quantmod,
##     quantreg, questionr, qvalue, R.cache, R.oo, R.utils, R6, ragg, ranger,
##     Rcpp, RcppArmadillo, RcppTOML, RCurl, readxl, recipes, reshape, rgl,
##     Rgraphviz, rlang, rmarkdown, robustbase, roxygen2, rprojroot, rsq, rstatix,
##     rstudioapi, rversions, rvest, S4Arrays, S4Vectors, sass, scales,
##     scatterpie, sctransform, sessioninfo, Seurat, SeuratObject, shadowtext,
##     shiny, sp, spam, SparseArray, spatstat.data, spatstat.explore,
##     spatstat.geom, spatstat.random, spatstat.univar, spatstat.utils, statmod,
##     stringi, stringr, styler, SummarizedExperiment, survminer, sva, svglite,
##     sys, systemfonts, TCGAbiolinks, TCGAbiolinksGUI.data, tensor, tensorflow,
##     testthat, textshaping, tfruns, TH.data, tibble, timeDate, tinytex, treeio,
##     tzdb, UCSC.utils, usethis, utf8, uwot, VIM, vroom, waldo, withr, xgboost,
##     XML, xml2, xts, XVector, yulab.utils, zeallot, zip, zlibbioc, zoo
## Old packages: 'curl', 'data.table', 'Hmisc', 'igraph', 'openssl', 'parallelly',
##   'promises', 'reticulate', 'RSQLite', 'xfun'
library(enrichplot)
BiocManager::install("STRINGdb")
## 'getOption("repos")' replaces Bioconductor standard repositories, see
## 'help("repositories", package = "BiocManager")' for details.
## Replacement repositories:
##     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
## Bioconductor version 3.20 (BiocManager 1.30.26), R 4.4.1 (2024-06-14)
## Warning: package(s) not installed when version(s) same as or greater than current; use
##   `force = TRUE` to re-install: 'STRINGdb'
## Installation paths not writeable, unable to update packages
##   path: /usr/local/lib/R/library
##   packages:
##     boot, class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv,
##     nlme, nnet, rpart, spatial, survival
##   path: /usr/local/lib/R/site-library
##   packages:
##     annotate, AnnotationDbi, ape, aplot, askpass, BH, Biobase, BiocFileCache,
##     BiocGenerics, BiocManager, BiocParallel, BiocVersion, biomaRt, Biostrings,
##     bit, bit64, bitops, Boruta, broom, bslib, C50, car, caret, checkmate, chk,
##     classInt, cli, clock, clue, clusterProfiler, colorspace, commonmark,
##     ComplexHeatmap, corrplot, cowplot, cpp11, credentials, crosstalk, Cubist,
##     cutpointr, dbplyr, dbscan, DelayedArray, DEoptimR, Deriv, DESeq2, devtools,
##     DiceKriging, diffobj, doBy, docopt, DOSE, dotCall64, downloader, DT,
##     dtplyr, edgeR, enrichplot, entropy, evaluate, fastDummies, fastmatch,
##     fgsea, fitdistrplus, fontawesome, forcats, fs, future, future.apply,
##     gargle, GDCRNATools, genefilter, generics, GenomeInfoDb, GenomeInfoDbData,
##     GenomicDataCommons, GenomicRanges, gert, ggforce, ggfun, ggnewscale,
##     ggplot2, ggplotify, ggpubr, ggraph, ggridges, ggsci, ggtree, gh, gld,
##     glmnet, globals, glue, GO.db, googledrive, googlesheets4, GOSemSim, gower,
##     GPArotation, gplots, graph, graphlayouts, gtable, hardhat, haven, HDO.db,
##     here, hms, httpuv, httr2, IRanges, jpeg, jsonlite, KEGGgraph, KEGGREST,
##     keras, KMsurv, knitr, labelled, later, lava, lavaan, lgr, limma, littler,
##     lme4, lmom, locfit, lubridate, magrittr, markdown, MatchIt, MatrixGenerics,
##     MatrixModels, matrixStats, maxstat, mice, mime, miniUI, mlbench, mlr3,
##     mlr3learners, mlr3measures, mlr3misc, mlr3pipelines, modeltools, multcomp,
##     mvtnorm, networkD3, nloptr, org.Hs.eg.db, party, partykit, patchwork,
##     pathview, pbapply, pbkrtest, pillar, pkgbuild, pkgdown, pkgload, plotly,
##     pROC, processx, prodlim, progressr, PRROC, ps, psych, purrr, quantmod,
##     quantreg, questionr, qvalue, R.cache, R.oo, R.utils, R6, ragg, ranger,
##     Rcpp, RcppArmadillo, RcppTOML, RCurl, readxl, recipes, reshape, rgl,
##     Rgraphviz, rlang, rmarkdown, robustbase, roxygen2, rprojroot, rsq, rstatix,
##     rstudioapi, rversions, rvest, S4Arrays, S4Vectors, sass, scales,
##     scatterpie, sctransform, sessioninfo, Seurat, SeuratObject, shadowtext,
##     shiny, sp, spam, SparseArray, spatstat.data, spatstat.explore,
##     spatstat.geom, spatstat.random, spatstat.univar, spatstat.utils, statmod,
##     stringi, stringr, styler, SummarizedExperiment, survminer, sva, svglite,
##     sys, systemfonts, TCGAbiolinks, TCGAbiolinksGUI.data, tensor, tensorflow,
##     testthat, textshaping, tfruns, TH.data, tibble, timeDate, tinytex, treeio,
##     tzdb, UCSC.utils, usethis, utf8, uwot, VIM, vroom, waldo, withr, xgboost,
##     XML, xml2, xts, XVector, yulab.utils, zeallot, zip, zlibbioc, zoo
## Old packages: 'curl', 'data.table', 'Hmisc', 'igraph', 'openssl', 'parallelly',
##   'promises', 'reticulate', 'RSQLite', 'xfun'
library(STRINGdb)

#Alternative Workflow with STRINGdb Integration in R
# Initialise the STRINGdb object for a specific organism
string_db <- STRINGdb$new(version = "12", species = 9606, score_threshold = 400, input_directory = "")

options(timeout = 600)  # increases to 10 minutes

# Gene mapping using STRINGdb
mapped_genes <- string_db$map(de_genes, "Symbol", removeUnmappedRows = TRUE)
## Warning:  we couldn't map to STRING 1% of your identifiers
# Recover interactions for mapped genes
interactions <- string_db$get_interactions(mapped_genes$STRING_id)

# Visualise the network using igraph or other visualisation tools
library(igraph)
## 
## Attaching package: 'igraph'
## The following object is masked from 'package:tibble':
## 
##     as_data_frame
## The following objects are masked from 'package:rtracklayer':
## 
##     blocks, path
## The following object is masked from 'package:BiocIO':
## 
##     path
## The following object is masked from 'package:Biostrings':
## 
##     union
## The following object is masked from 'package:XVector':
## 
##     path
## The following object is masked from 'package:circlize':
## 
##     degree
## The following objects are masked from 'package:topGO':
## 
##     algorithm, graph
## The following objects are masked from 'package:graph':
## 
##     degree, edges, intersection, union
## The following object is masked from 'package:clusterProfiler':
## 
##     simplify
## The following object is masked from 'package:tidyr':
## 
##     crossing
## The following objects are masked from 'package:dplyr':
## 
##     as_data_frame, groups, union
## The following object is masked from 'package:GenomicRanges':
## 
##     union
## The following object is masked from 'package:IRanges':
## 
##     union
## The following object is masked from 'package:S4Vectors':
## 
##     union
## The following objects are masked from 'package:BiocGenerics':
## 
##     normalize, path, union
## The following objects are masked from 'package:stats':
## 
##     decompose, spectrum
## The following object is masked from 'package:base':
## 
##     union
g <- graph_from_data_frame(interactions, directed=FALSE)
plot(g)

# Detect clusters (e.g. Louvain)
clusters <- cluster_louvain(g)

# Plot with colours by cluster
plot(g, vertex.color=clusters$membership)

# Perform GO enrichment analysis
# Biological Process
# Ensure you have the packages installed
library(clusterProfiler)
library(org.Hs.eg.db)
library(ggplot2)
library(dplyr) # For data manipulation


# Biological Process
enrich_result <- enrichGO(gene = mapped_genes$Symbol,
                          OrgDb = org.Hs.eg.db,
                          keyType = "SYMBOL",
                          ont = "BP", # Biological Ontology. It can be ‘BP’, “MF”, or ‘CC’
                          pAdjustMethod = "BH", # Benjamini-Hochberg (BH) is the same as FDR.
                          pvalueCutoff = 0.05,
                          qvalueCutoff = 0.2)


if (is.null(enrich_result) || nrow(as.data.frame(enrich_result)) == 0) {
  print("No significantly enriched GO terms were found with the provided criteria.")
} else {
  plot_data <- as.data.frame(enrich_result) %>%
    arrange(p.adjust) %>%
    head(15) # Display the 15 most significant terms
  
  # Create a numeric column for the Y axis to use with geom_segment
  # The order of the terms on the Y axis is important.
  plot_data$y_pos <- rev(seq_along(plot_data$Description)) # To sort from top to bottom
  
  ggplot(plot_data, aes(x = Count, y = y_pos)) + # Use y_pos for the Y axis
    # Add geom_segment for the ‘threads’
    # It starts at x=0 (or a small value) and goes up to the Count of the term.
    geom_segment(aes(x = 0, xend = Count, y = y_pos, yend = y_pos),
                 color = "gray", linewidth = 0.5) +
    geom_point(aes(size = Count, color = p.adjust), alpha = 0.8) +
    scale_color_gradientn(
      colors = c("darkblue", "steelblue", "lightblue", "lightgreen", "yellow", "orange", "darkred"),
      name = "FDR",
      trans = "log10",
      breaks = scales::trans_breaks("log10", function(x) 10^x),
      labels = scales::trans_format("log10", scales::math_format(10^.x))
    ) +
    scale_size_area(max_size = 15, name = "Contagem de Genes") +
    # Map labels back to GO descriptions
    scale_y_continuous(breaks = plot_data$y_pos, labels = plot_data$Description) +
    labs(
      title = "GO Enrichment Analysis (Biological Processes)",
      x = "Genes Counting",
      y = "GO Terms (Biological Processes)"
    ) +
    theme_minimal() +
    theme(
      axis.text.y = element_text(size = 12, face = "bold"),
      axis.title = element_text(size = 14, face = "bold"),
      plot.title = element_text(size = 16, face = "bold", hjust = 0.5),
      legend.position = "right",
      legend.title = element_text(size = 12, face = "bold"),
      legend.text = element_text(size = 10),
      panel.grid.major.y = element_blank(), # Remove the default horizontal grid lines
      panel.grid.minor = element_blank(),
      panel.border = element_rect(colour = "black", fill=NA, linewidth=1)
    )
}

barplot(enrich_result, showCategory = 10, title= "GO Enrichment Analysis")
## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?
## Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`.
## ℹ See also `vignette("ggplot2-in-packages")` for more information.
## ℹ The deprecated feature was likely used in the enrichplot package.
##   Please report the issue at
##   <https://github.com/GuangchuangYu/enrichplot/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

# Network graph of enriched terms
cnetplot(enrich_result, showCategory = 10)
## Warning: `aes_()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`
## ℹ The deprecated feature was likely used in the enrichplot package.
##   Please report the issue at
##   <https://github.com/GuangchuangYu/enrichplot/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# Heatmap
heatplot(enrich_result, showCategory = 10)

# Perform KEGG enrichment analysis
ekegg <- enrichKEGG(gene = mapped_genes$ENTREZID, organism = "hsa", pAdjustMethod = "BH", qvalueCutoff = 0.05)
## Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
## Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
# Generate GO/STRING style bubble chart
if (is.null(ekegg) || nrow(as.data.frame(ekegg)) == 0) {
  print("No significantly enriched KEGG pathways were found with the criteria provided.")
} else {
  plot_data_kegg <- as.data.frame(ekegg) %>%
    arrange(p.adjust) %>% # Sort by p.adjust (FDR)
    head(15) # Selects the 15 most significant pathways to plot

  # Creates a numerical position for the terms on the Y-axis, to control the order and lines
  plot_data_kegg$y_pos <- rev(seq_along(plot_data_kegg$Description)) # reverse to the most significant at the top
  
  # Starting to build the graph with ggplot2
  ggplot(plot_data_kegg, aes(x = Count, y = y_pos)) +
    # Adds the connection lines (wires) from the Y-axis to the bubble.
    geom_segment(aes(x = 0, xend = Count, y = y_pos, yend = y_pos),
                 color = "gray80", linewidth = 0.6) + # Softer colour for the lines
    # Add the bubbles
    geom_point(aes(size = Count, color = p.adjust), alpha = 0.9) +
    # Colour scale configuration for FDR (p.adjust)
    scale_color_gradientn(
      colors = c("darkblue", "steelblue", "lightblue", "lightgreen", "yellow", "orange", "darkred"),
      name = "FDR",
      trans = "log10", # Use logarithmic scale for FDR
      breaks = scales::trans_breaks("log10", function(x) 10^x), # Breaks in scientific notation captions
      labels = scales::trans_format("log10", scales::math_format(10^.x)), # Scientific notation format
      limits = c(min(plot_data_kegg$p.adjust), max(plot_data_kegg$p.adjust)) # Sets limits for data
    ) +
    # Size scale configuration for Gene Counting
    scale_size_area(
      max_size = 18, # Maximum bubble size
      name = "Gene count", # Caption title size
      breaks = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0)))), # Suggests reasonable breaks
      labels = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0))))
    ) +
    # Maps the Y-axis labels back to the KEGG pathway descriptions
    scale_y_continuous(
      breaks = plot_data_kegg$y_pos,
      labels = plot_data_kegg$Description
    ) +
    # Labels and Chart Title
    labs(
      title = "KEGG Pathway Enrichment Analysis",
      x = "Gene count", # X-axis is now Gene Count
      y = "KEGG Pathway" # Y-axis is the name of the pathway
    ) +
    # Chart Theme and Style
    theme_minimal() +
    theme(
      axis.text.y = element_text(size = 12, face = "bold"), # KEGG terms in bold and larger font
      axis.title = element_text(size = 14, face = "bold"), # Axis titles
      plot.title = element_text(size = 16, face = "bold", hjust = 0.5), # Centred title
      legend.position = "right", # Position of subtitles
      legend.title = element_text(size = 12, face = "bold"),
      legend.text = element_text(size = 10),
      panel.grid.major.y = element_blank(), # Remove standard horizontal grid lines
      panel.grid.minor = element_blank(), # Remove minor grid liness
      panel.border = element_rect(colour = "black", fill=NA, linewidth=1.2) # Black border around the plot
    )
} 

barplot(ekegg, showCategory = 10, title = "KEGG Enrichment Analysis")
## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?

# Network graph of enriched terms
cnetplot(ekegg, showCategory = 10)

# Heatmap
heatplot(ekegg, showCategory = 10)

7.Transcription factors in the analysis between non-lesion PsA vs lesion PsA

# Load the necessary packages
library(GenomicFeatures)
## 
## Attaching package: 'GenomicFeatures'
## The following object is masked from 'package:topGO':
## 
##     genes
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)
library(JASPAR2020)
library(TFBSTools)
library(SummarizedExperiment)
library(motifmatchr)

# Load the TxDb database
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

# Extraction of exons by gene
exons_by_gene <- exonsBy(txdb, by = "gene")

# Obtain the coordinates of the genes (taking the first and last positions of the exons)
genes_info <- range(exons_by_gene)

# Obtain transcription information
transcripts_info <- transcripts(txdb)

# Map genes of interest to Entrez IDs (replace “de_genes” with the actual list of genes)
gene_entrez <- mapIds(org.Hs.eg.db, keys = mapped_genes$Symbol, column = "ENTREZID", keytype = "SYMBOL", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Filter the genes of interest
promoters_info <- subset(genes_info, names(genes_info) %in% gene_entrez)

# Define promoter regions (2 kb upstream of TSS)
promoters <- promoters(promoters_info, upstream = 2000, downstream = 0)
## Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 1 out-of-bound range located on sequence
##   chr2_GL383522v1_alt. Note that ranges located on a sequence whose
##   length is unknown (NA) or on a circular sequence are not considered
##   out-of-bound (use seqlengths() and isCircular() to get the lengths and
##   circularity flags of the underlying sequences). You can use trim() to
##   trim these ranges. See ?`trim,GenomicRanges-method` for more
##   information.
# Filter the main chromosomes
promoters <- keepStandardChromosomes(promoters, pruning.mode = "coarse")

# Remove any regions that exceed the limits of the chromosomes.
promoters <- trim(promoters)

# Convert CompressedGRangesList promoters to GRanges
promoters_gr <- unlist(promoters)

# Load the JASPAR grounds database
motifs <- getMatrixSet(JASPAR2020, opts = list(species = "Homo sapiens"))

# Create a data frame with the IDs of the reasons and their names (TFs)
motif_info <- data.frame(
  motif_id = names(motifs),
  tf_name = sapply(motifs, function(x) x@name),
  stringsAsFactors = FALSE
)

# Enriching motifs in promoting regions
motifHits <- matchMotifs(motifs, promoters_gr, genome = BSgenome.Hsapiens.UCSC.hg38)

# Count the number of occurrences of the reasons in each promoting region.
motif_counts <- countOverlaps(promoters_gr, motifHits)

# Add counts to GRanges with promoting regions
promoters_gr$motif_counts <- motif_counts

# Summary of motif counts
summary(promoters_gr$motif_counts)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.0000  0.0000  0.4825  1.0000  1.0000
# Obtain the names of the motifs and TFs
motif_names <- names(motifHits)

# Extract the reason table from the RangedSummarizedExperiment object
motif_data <- assays(motifHits)[[1]] # Assuming that the table of reasons is in the first list of assays

# Obtain information about TFs
# The names of TFs may be in the colnames or in associated metadata
tf_names <- colnames(motif_data)  

# Add the reason count if available
motif_counts <- rowSums(motif_data) 

# Check the dimensions of the motif_data object
dim(motif_data) # Number of rows and columns
## [1] 114 633
# Check the length of tf_names and motif_counts
tf_names_length <- length(tf_names)
motif_counts_length <- length(motif_counts)

# Print the lengths for diagnosis
cat("Length of tf_names:", tf_names_length, "\n")
## Length of tf_names: 633
cat("Length of motif_counts:", motif_counts_length, "\n")
## Length of motif_counts: 114
# Verify that the dimensions of motif_data correspond to the number of TFs and motifs
motif_data_dims <- dim(motif_data)
cat("Dimensions of motif_data (rows, columns):", motif_data_dims, "\n")
## Dimensions of motif_data (rows, columns): 114 633
# Check whether the number of reasons is greater or lesser
if (tf_names_length > motif_counts_length) {
  # Check additional columns
  tf_names <- tf_names[1:motif_counts_length] # Adjust to the length of motif_counts
} else {
  # Adjust motif_counts to match tf_names
  motif_counts <- motif_counts[1:tf_names_length]
}

# Now, create the data frame with adjusted lengths
motif_summary <- data.frame(
  tf_name = tf_names,
  motif_count = motif_counts
)

# Check the correspondence between TF names and the columns in motif_data
all(tf_names %in% colnames(motif_data)) # Should return TRUE if all TF names are present
## [1] TRUE
# Sort and identify key TFs
tf_summary <- motif_summary[order(motif_summary$motif_count, decreasing = TRUE), ]
top_tf_summary <- head(tf_summary, 121) # Adjust the number as required

# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(top_tf_summary), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Replace rownames with gene symbols
rownames(top_tf_summary) <- gene_symbols

# Add reason ID as a column
top_tf_summary$motif_id <- rownames(top_tf_summary)

# Add to the table of TF names
motif1 <- merge(top_tf_summary, motif_info, by.x = "tf_name", by.y = "motif_id")

# Reorder columns
motif2 <- motif1[, c("motif_id", "tf_name.y", "motif_count")]
colnames(motif2) <- c("motif_id", "tf_name", "motif_count")

# Sort by frequency (motif_count) in descending order
motif2 <- motif2 %>% arrange(desc(motif_count))

print(motif2)
##     motif_id             tf_name motif_count
## 1      CCL20                IRF8         236
## 2      CXCL8                 YY1         204
## 3       CCR7               RREB1         196
## 4      CCND1                 GSC         181
## 5       GJB6         MZF1(var.2)         176
## 6      CXCL2              POU2F2         173
## 7        PI3                ELF5         170
## 8        IL5               STAT3         168
## 9       FUT2                 FOS         167
## 10      IFI6               FOSL2         167
## 11       NMI              NKX2-3         166
## 12      PRF1               FOXL1         165
## 13      DKK1          RARA::RXRA         165
## 14   TNFRSF9              SREBF2         164
## 15      GZMA        STAT1::STAT2         163
## 16    TGFBR3              MLXIPL         161
## 17    ZNF316               FOXF2         160
## 18    FCGR3A               INSM1         159
## 19     PINK1                LHX6         159
## 20     SAMD9                ETV6         158
## 21   EFCAB13                SOX9         157
## 22      MEFV              NFATC3         157
## 23   PLA2G4D           MAF::NFE2         154
## 24     PLIN5                SHOX         154
## 25     PPARG                 EN2         154
## 26      RORC                HEY2         154
## 27     IL12B              SREBF1         152
## 28     PRDM1                IRF9         152
## 29    FAXDC2            MAX::MYC         150
## 30      WNK1               MEOX1         150
## 31     MUCL1         RORA(var.2)         149
## 32     IL17F                PBX1         148
## 33   SLC7A11         ARNT::HIF1A         146
## 34     APOL6             NEUROD2         146
## 35       IL6         GATA1::TAL1         145
## 36  SERPINB1          EWSR1-FLI1         145
## 37      IRS1               DMRT3         143
## 38      IL37               MEF2C         140
## 39      OLR1               CENPB         140
## 40      NOD2         JDP2(var.2)         140
## 41     CTLA4                 SRY         139
## 42     RSAD2              NKX2-8         139
## 43      GJB2         JUND(var.2)         138
## 44    AKAP13                PAX6         136
## 45       LYZ                LBX1         136
## 46      SYT1                 MLX         136
## 47    S100A8               HINFP         135
## 48     IL2RA               STAT1         135
## 49    IL36RN          JUN(var.2)         135
## 50      JRKL                NFIX         135
## 51  PPARGC1A               PPARG         134
## 52      GBP5                RORA         134
## 53     IL17A               THAP1         134
## 54      IL21               GRHL1         134
## 55      CRB1               NR4A2         133
## 56      MMP1              POU6F1         133
## 57      XAF1                ESX1         133
## 58     HYAL4               PLAG1         132
## 59    NT5C3A                 DBP         132
## 60       ALB                REST         131
## 61      EGR3                CTCF         130
## 62     IL23A                ELF4         130
## 63      NOS2             BHLHE41         129
## 64     PTGS2                GCM1         129
## 65     APOL1                NFIA         129
## 66    CYP1A1          TAL1::TCF3         128
## 67     GATA3               FOXH1         128
## 68      IL22               CREB3         128
## 69      SELL                 ISX         128
## 70     CENPK                JDP2         128
## 71      YOD1               FOXI1         126
## 72       PLG                 EN1         125
## 73       EGF          NFIC::TLX1         125
## 74    ZNF415               FOXO3         125
## 75     CD274                NRF1         125
## 76      GZMB              TCF7L2         125
## 77     CAPS2             NEUROG2         125
## 78     HCAR3               NHLH1         123
## 79      CD38                PAX4         122
## 80      GBP1                 JUN         122
## 81      ICOS SMAD2::SMAD3::SMAD4         122
## 82     CXCR2               FOXP2         122
## 83      TYMP         NR1H2::RXRA         121
## 84      FRZB                DUX4         121
## 85      ACP7               FOXG1         121
## 86      NKG7              BARHL2         121
## 87     ACKR2           RXRA::VDR         120
## 88       GPT               NR2C2         120
## 89     FOSL1                MYF6         120
## 90      IL1B                IRF1         119
## 91     HERC6                FLI1         119
## 92     KANK4                RELA         117
## 93   S100A12               HNF1B         117
## 94     NAMPT               FOXD1         116
## 95     CALD1                 MSC         116
## 96     IFIT3                ELK4         115
## 97      IFNG                ESR2         115
## 98    CXCL10                KLF5         114
## 99   ZC3H12A                MSX1         114
## 100      MX1                ALX3         113
## 101   FCGR1A              NFATC2         112
## 102   ZNF483                 REL         111
## 103   S100A9               HNF1A         109
## 104    CSMD1               KLF13         109
## 105    STAT1               MIXL1         107
## 106    S100P              HOXC11         105
## 107   SLC1A2               MEF2B         104
## 108     CD8A              NKX6-1         103
## 109   CXCL13                IRF2         102
## 110     CCL2                HSF1         102
## 111   CLEC4D              ZBTB33         101
## 112     AIM2               OLIG2         100
## 113     EGFR             ZNF354C          90
## 114     CD80              NKX6-2          86

8. Comparison between normal skin in ankylosing spondylitis versus damaged skin in psoriatic arthritis

# Wald test to obtain contrast-specific results
dsd <- DESeq(dsa, test = "Wald", sfType = "poscount")
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
r <- results(dsd, contrast = c("Group", groups[3], groups[2]), alpha = 0.05, pAdjustMethod = "fdr")

groups <- levels(colData(dsd)$Group)

df <- as.data.frame(r)

# Filter only significant genes
sig_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) >= 1)

# volcano plot
old.pal <- palette(c("#00BFFF", "#FF3030")) # low-hi colors
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log2FoldChange, -log10(padj), main=paste(groups[3], "vs", groups[2]),
       xlab="log2FC", ylab="-log10(Padj)", pch=20, cex=0.5)
  text(log2FoldChange, -log10(padj), labels=rownames(r), cex=0.6, pos=4)
})
with(subset(r, padj<0.05 & abs(log2FoldChange) >= 1),
     points(log2FoldChange, -log10(padj), pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1))
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20,col=1:2)

# Plot only significant genes
# MD PLOT
par(mar=c(4,4,2,1), cex.main=1.5)
with(sig_genes, {
  plot(log10(baseMean), log2FoldChange,
       main=paste(groups[3], "vs", groups[2]),
       xlab="log10(mean of normalized counts)", ylab="log2FoldChange",
       pch=20, col=(sign(log2FoldChange) + 3)/2, cex=1)
  text(log10(baseMean), log2FoldChange, labels=rownames(sig_genes), cex=0.6, pos=4)
})
legend("bottomleft", title=paste("Padj<", 0.05, sep=""), legend=c("down", "up"), pch=20, col=1:2)
abline(h=0)

palette(old.pal) # restore palette

# Add gene symbols to the points on the graph
# Install the packages if you do not already have them
library(ggplot2)
library(ggrepel)

plotVolcano <- function(res, title = "Volcano Plot") {
  res$group <- "NS"
  res$group[res$padj < 0.05 & res$log2FoldChange > 1] <- "Up"
  res$group[res$padj < 0.05 & res$log2FoldChange < -1] <- "Down"
  
  res$label <- ifelse(res$group != "NS", rownames(res), NA)
  
  ggplot(res, aes(x = log2FoldChange, y = -log10(padj), color = group)) +
    geom_point(alpha = 0.7, size = 2) +
    geom_hline(yintercept = -log10(0.05), linetype = "dashed") +
    geom_vline(xintercept = c(-1, 1), linetype = "dashed") +
    scale_color_manual(values = c("Up" = "firebrick", "Down" = "dodgerblue", "NS" = "grey80")) +
    ggrepel::geom_text_repel(aes(label = label), size = 3, max.overlaps = Inf) +
    theme_minimal() +
    labs(title = title, x = "log2 Fold Change", y = "-log10 adjusted p-value", color = "Regulation")
}

# Example of function usage
plotVolcano(r, paste(groups[3], "vs", groups[2]))
## Warning: Removed 4 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 300 rows containing missing values or values outside the scale range
## (`geom_text_repel()`).

# Genes upregulated
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange >= 1))

# Genes downregulated
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange <= -1))

# All DEGs with |log2FC| > 2
de_genes <- c(up_genes, down_genes)

expr_datasa <- as.data.frame(expr_data[rownames(expr_data) %in% de_genes, ])

# Convert expression data to long format for ggplot2
expr_datas <- as.data.frame(expr_datasa)
expr_datas$Gene <- rownames(expr_datas)
expr_datas <- pivot_longer(expr_datas, cols = -Gene, names_to = "Sample", values_to = "Expression")
expr_datas <- merge(expr_datas, pheno_data, by.x = "Sample", by.y = "geo_accession")

# Check column names and a sample of the data
expresse <- r[order(r$padj)[1:429], ]
expresse <- merge(as.data.frame(expresse), expr_datasa, by = 0, sort = F)


library(dplyr)
library(tibble)
library(clusterProfiler)
library(ggplot2)

r_df <- as.data.frame(r)

# Assuming that “r_df” is your data frame with the DESeq2 results

# This ensures that gene names are preserved.
r_df_com_genes <- r_df %>%
  rownames_to_column(var = "Gene") 

top30_fc <- r_df_com_genes %>%
  dplyr::filter(padj < 0.05 & abs(log2FoldChange) > 1) %>%
  dplyr::arrange(desc(abs(log2FoldChange))) %>%
  dplyr::slice(1:30) %>%
  dplyr::mutate(
    Regulation = case_when(
      log2FoldChange > 1 ~ "Upregulated",
      log2FoldChange < -1 ~ "Downregulated"
    )
  )

# Chart with positive and negative bars
ggplot(top30_fc, aes(x = reorder(Gene, log2FoldChange), y = log2FoldChange, fill = Regulation)) +
  geom_col() +
  coord_flip() + # Place the genes on the Y axis
  scale_fill_manual(values = c("Upregulated" = "steelblue", "Downregulated" = "tomato")) +
  scale_y_continuous(breaks = seq(-8, 4, by = 1)) + # Adjust the limits if necessary.
  theme_bw() +
  labs(
    title = "The 30 most prominent DEGs between normal skin AS and lesion PsA (GSE186063)",
    x = "Gene",
    y = "log2 Fold Change",
    fill = "Regulation"
  ) + 
  theme(
    axis.text.y = element_text(color = "black", face = "bold", size = 9)
  )

# --- Selects the 20 MOST overexpressed genes ---
up_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange > 1) %>%
  arrange(desc(log2FoldChange)) %>% 
  head(20) %>%
  pull(Row.names)

# --- Filters expression data ---
expr_datas_filtrado_up <- expr_datas %>%
  filter(`diagnosis:ch1` %in% c("Psoriatic Arthritis", "Ankylosing Spondylitis")) %>%
  filter(`source_name_ch1` %in% c("lesion", "normal skin")) %>% 
  filter(Gene %in% up_20genes)

# --- Calculates the average per gene and per group  ---
expr_datasa_up <- expr_datas_filtrado_up %>%
  group_by(Gene, `source_name_ch1`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    sd_expression = sd(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “non-lesion” group
dados_para_plotar_up <- expr_datasa_up %>%
  filter(source_name_ch1 == "normal skin")

# --- Graph Generation ---
ggplot(dados_para_plotar_up, aes(x = mean_expression, y = reorder(Gene, mean_expression))) +
  geom_col(fill = "steelblue", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Upregulated Genes in Normal Skin", # Clearer title
    subtitle = "For normal skin AS vs lesion PsA (GSE186063)",
    x = "Average Expression in the Group 'Normal skin'", # Clearer axle label
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- Selects the 20 MOST under-expressed genes ---
down_20genes <- expresse %>%
  filter(padj < 0.05 & log2FoldChange < -1) %>%
  arrange(log2FoldChange) %>% # <-- Sort from most negative to least negative
  head(20) %>%
  pull(Row.names)

# --- Filters expression data for genes and groups of interest ---
expr_datas_filtrado_down <- expr_datas %>%
  filter(`diagnosis:ch1` %in% c("Psoriatic Arthritis", "Ankylosing Spondylitis")) %>%
  filter(`source_name_ch1` %in% c("lesion", "normal skin")) %>% 
  filter(Gene %in% down_20genes)

# --- Calculates the average per gene and per group ---
expr_datasa_down <- expr_datas_filtrado_down %>%
  group_by(Gene, `source_name_ch1`) %>%
  summarise(
    mean_expression = mean(Expression, na.rm = TRUE),
    .groups = 'drop'
  )

# --- Preparation for the chart ---
# Filter to show the average expression ONLY in the “lesion” group
dados_para_plotar <- expr_datasa_down %>%
  filter(source_name_ch1 == "normal skin")

# --- Graph Generation ---
ggplot(dados_para_plotar, aes(x = mean_expression, y = reorder(Gene, -mean_expression))) +
  geom_col(fill = "red", color = "black", width = 0.7) +
  labs(
    title = "Average Expression of the Main Downregulated Genes in Non-Lesion Skin", # Clearer title
    subtitle = "For normal skin AS vs lesion PsA (GSE186063)",
    x = "Average Expression in the Group 'Normal skin'", # Clearer axle label
    y = "Gene"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    panel.grid.major.y = element_blank(),
    axis.text.y = element_text(size = 12)
  )

# --- The code to create 'count_array' ---
up_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange > 1))
down_genes <- rownames(subset(r, padj < 0.05 & log2FoldChange < -1))
genes_interesse <- c(up_genes, down_genes)

expr_filtrado <- expr_datas %>%
  filter(`diagnosis:ch1` %in% c("Psoriatic Arthritis", "Ankylosing Spondylitis")) %>%
  filter(`source_name_ch1` %in% c("lesion", "normal skin")) %>% 
  filter(Gene %in% genes_interesse)

matriz_contagem <- expr_filtrado %>%
  select(Gene, Sample, Expression) %>%
  pivot_wider(names_from = Sample, values_from = Expression, values_fill = 0) %>%
  column_to_rownames(var = "Gene")

# Filter your original “sample_info” object to keep only the samples that are in your final matrix
# This ensures that the annotation corresponds exactly to the heatmap data
sample_info_filtrado <- subset(sample_info, rownames(sample_info) %in% colnames(matriz_contagem))


# Select the 20 most highly expressed genes
media_dos_genes <- rowMeans(matriz_contagem)
media_ordenada <- sort(media_dos_genes, decreasing = TRUE)
top_20_genes_por_media <- names(head(media_ordenada, 20))
heatmapData_top20 <- as.matrix(matriz_contagem[top_20_genes_por_media, ])


# Create the annotation for the heatmap from the filtered and corrected information
annotation_data <- data.frame(
  Group = sample_info_filtrado$Group,
  row.names = rownames(sample_info_filtrado)
)

# Ensure that the order of the columns in the heatmap and annotation is the same
heatmapData_top20 <- heatmapData_top20[, rownames(annotation_data)]


# --- Heatmap generation with ComplexHeatmap ---

# Rescale data by row (Z-score)
mat_scaled <- t(scale(t(heatmapData_top20)))

# Create the column annotation
ha_col <- HeatmapAnnotation(
  Group = annotation_data$Group,
  col = list(Group = c("normal.skin.AS" = "#1f77b4", "lesion.PsA" = "#d62728"))
)

# Define the colour palette
cores <- colorRamp2(c(-2, 0, 2), rev(RColorBrewer::brewer.pal(3, "RdBu")))

# Generate the heatmap
Heatmap(
  mat_scaled,
  name = "Z-score",
  top_annotation = ha_col,
  col = cores,
  
  # Divide the columns into groups for clearer viewing
  column_split = annotation_data$Group,
  
  cluster_rows = TRUE,
  cluster_columns = TRUE, # Cluster within each divided group
  
  show_column_names = FALSE,
  show_row_names = TRUE,
  column_title = "Heatmap of the 20 most highly expressed DEGs (normal skin AS vs. lesion PsA GSE186063)",
  heatmap_legend_param = list(title = "Z-score")
)

# Filter differentially expressed genes
de_genes <- subset(r, padj < 0.05 & abs(log2FoldChange) > 1)

#Create a data frame from de_genes
de_genes <- data.frame(de_genes)

# Suppose your dataframe is called df and you want to select columns ‘column1’, “column2” and ‘column3’
de_genes <- de_genes %>% select(log2FoldChange, padj)

# Assuming that rownames(df) are gene symbols
gene_symbols <- rownames(de_genes)

# Convert gene symbols to Entrez IDs
gene_entrez_ids <- bitr(gene_symbols, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)
## 'select()' returned 1:1 mapping between keys and columns
# First, convert the rownames from df into a column
de_genes$Symbol <- rownames(de_genes)

# Performs the join between the original table and the converted IDs
de_genes <- merge(de_genes, gene_entrez_ids, by.x = "Symbol", by.y = "SYMBOL", all.x = TRUE)

# Ensure unique symbols
de_genes <- de_genes[!duplicated(de_genes$ENTREZID), ]

# Alternative Workflow with STRINGdb Integration in R
# Initialise the STRINGdb object for a specific organism
string_db <- STRINGdb$new(version = "12", species = 9606, score_threshold = 400, input_directory = "")

options(timeout = 600)  # increases to 10 minutes

# Gene mapping using STRINGdb
mapped_genes <- string_db$map(de_genes, "Symbol", removeUnmappedRows = TRUE)
## Warning:  we couldn't map to STRING 1% of your identifiers
# Recover interactions for mapped genes
interactions <- string_db$get_interactions(mapped_genes$STRING_id)

# Visualise the network using igraph or other visualisation tools
library(igraph)
g <- graph_from_data_frame(interactions, directed=FALSE)
plot(g)

# Detect clusters (e.g. Louvain)
clusters <- cluster_louvain(g)

# Plot with colours by cluster
plot(g, vertex.color=clusters$membership)

# Perform GO enrichment analysis
# Biological Process
enrich_result <- enrichGO(gene = mapped_genes$Symbol,
                          OrgDb = org.Hs.eg.db,
                          keyType = "SYMBOL",
                          ont = "BP", # Biological Ontology. It can be ‘BP’, “MF”, or ‘CC’.
                          pAdjustMethod = "BH",
                          pvalueCutoff = 0.05,
                          qvalueCutoff = 0.2)

barplot(enrich_result, showCategory = 10, title= "GO Enrichment Analysis")
## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?

# Network graph of enriched terms
cnetplot(enrich_result, showCategory = 10)
## Warning: ggrepel: 3 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# Heatmap
heatplot(enrich_result, showCategory = 10)

# Perform KEGG enrichment analysis
ekegg <- enrichKEGG(gene = mapped_genes$ENTREZID, organism = "hsa", pAdjustMethod = "BH", qvalueCutoff = 0.05)

# Generate GO/STRING style bubble chart
if (is.null(ekegg) || nrow(as.data.frame(ekegg)) == 0) {
  print("No significantly enriched KEGG pathways were found with the criteria provided.")
} else {
  plot_data_kegg <- as.data.frame(ekegg) %>%
    arrange(p.adjust) %>% # Sort by p.adjust (FDR)
    head(15) # Selects the 15 most significant pathways to plot

  # Creates a numerical position for the terms on the Y-axis, to control the order and lines
  plot_data_kegg$y_pos <- rev(seq_along(plot_data_kegg$Description)) # reverse to the most significant at the top
  
  # Starting to build the graph with ggplot2
  ggplot(plot_data_kegg, aes(x = Count, y = y_pos)) +
    # Adds the connection lines (wires) from the Y-axis to the bubble
    geom_segment(aes(x = 0, xend = Count, y = y_pos, yend = y_pos),
                 color = "gray80", linewidth = 0.6) + # Softer colour for the lines
    # Add the bubbles
    geom_point(aes(size = Count, color = p.adjust), alpha = 0.9) +
    # Colour scale configuration for FDR (p.adjust)
    scale_color_gradientn(
      colors = c("darkblue", "steelblue", "lightblue", "lightgreen", "yellow", "orange", "darkred"),
      name = "FDR",
      trans = "log10", # Use logarithmic scale for FDR
      breaks = scales::trans_breaks("log10", function(x) 10^x), # Breaks in scientific notation captions
      labels = scales::trans_format("log10", scales::math_format(10^.x)), # Scientific notation format
      limits = c(min(plot_data_kegg$p.adjust), max(plot_data_kegg$p.adjust)) # Sets limits for data
    ) +
    # Size scale configuration for Gene Counting
    scale_size_area(
      max_size = 18, # Maximum bubble size
      name = "Gene count", # Caption title size
      breaks = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0)))), # Suggests reasonable breaks
      labels = unique(round(quantile(plot_data_kegg$Count, probs = c(0.25, 0.5, 0.75, 1.0))))
    ) +
    # Maps the Y-axis labels back to the KEGG pathway descriptions
    scale_y_continuous(
      breaks = plot_data_kegg$y_pos,
      labels = plot_data_kegg$Description
    ) +
    # Labels and Chart Title
    labs(
      title = "KEGG Pathway Enrichment Analysis",
      x = "Gene count", # X-axis is now Gene Count
      y = "KEGG Pathway" # Y-axis is the name of the pathway
    ) +
    # Chart Theme and Style
    theme_minimal() +
    theme(
      axis.text.y = element_text(size = 12, face = "bold"), # KEGG terms in bold and larger font
      axis.title = element_text(size = 14, face = "bold"), # Axis titles
      plot.title = element_text(size = 16, face = "bold", hjust = 0.5), # Centred title
      legend.position = "right", # Position of subtitles
      legend.title = element_text(size = 12, face = "bold"),
      legend.text = element_text(size = 10),
      panel.grid.major.y = element_blank(), # Remove standard horizontal grid lines
      panel.grid.minor = element_blank(), # Remove smaller grid lines
      panel.border = element_rect(colour = "black", fill=NA, linewidth=1.2) # Black border around the plot
    )
} 

barplot(ekegg, showCategory = 10, title = "KEGG Enrichment Analysis")
## Warning in fortify(object, showCategory = showCategory, by = x, ...): Arguments in `...` must be used.
## ✖ Problematic argument:
## • by = x
## ℹ Did you misspell an argument name?

# Network graph of enriched terms
cnetplot(ekegg, showCategory = 10)
## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# Heatmap
heatplot(ekegg, showCategory = 10)

9. Transcription factors between the analysis of normal AS skin vs PsA lesion

# Load the TxDb database
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

# Extraction of exons by gene
exons_by_gene <- exonsBy(txdb, by = "gene")

# Obtain the coordinates of the genes (taking the first and last positions of the exons)
genes_info <- range(exons_by_gene)

# Obtain transcription information
transcripts_info <- transcripts(txdb)

# Map genes of interest to Entrez IDs (replace “de_genes” with the actual list of genes)
gene_entrez <- mapIds(org.Hs.eg.db, keys = mapped_genes$Symbol, column = "ENTREZID", keytype = "SYMBOL", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Filter the genes of interest
promoters_info <- subset(genes_info, names(genes_info) %in% gene_entrez)

# Define promoter regions (2 kb upstream of TSS)
promoters <- promoters(promoters_info, upstream = 2000, downstream = 0)
## Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 1 out-of-bound range located on sequence
##   chr2_GL383522v1_alt. Note that ranges located on a sequence whose
##   length is unknown (NA) or on a circular sequence are not considered
##   out-of-bound (use seqlengths() and isCircular() to get the lengths and
##   circularity flags of the underlying sequences). You can use trim() to
##   trim these ranges. See ?`trim,GenomicRanges-method` for more
##   information.
# Filter the main chromosomes
promoters <- keepStandardChromosomes(promoters, pruning.mode = "coarse")

# Remove any regions that exceed the limits of the chromosomes.
promoters <- trim(promoters)

# Convert CompressedGRangesList promoters to GRanges
promoters_gr <- unlist(promoters)

# Load the JASPAR grounds database
motifs <- getMatrixSet(JASPAR2020, opts = list(species = "Homo sapiens"))

# Create a data frame with the IDs of the reasons and their names (TFs)
motif_info <- data.frame(
  motif_id = names(motifs),
  tf_name = sapply(motifs, function(x) x@name),
  stringsAsFactors = FALSE
)

# Enriching motifs in promoting regions
motifHits <- matchMotifs(motifs, promoters_gr, genome = BSgenome.Hsapiens.UCSC.hg38)

# Count the number of occurrences of the reasons in each promoting region
motif_counts <- countOverlaps(promoters_gr, motifHits)

# Add counts to GRanges with promoting regions
promoters_gr$motif_counts <- motif_counts

# Summary of motif counts
summary(promoters_gr$motif_counts)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.0000  0.0000  0.4833  1.0000  1.0000
# Obtain the names of the motifs and TFs
motif_names <- names(motifHits)

# Extract the reason table from the RangedSummarizedExperiment object
motif_data <- assays(motifHits)[[1]] # Assuming that the table of reasons is in the first list of assays

# Obtain information about TFs
# The names of the TFs can be in the colnames or in associated metadata
tf_names <- colnames(motif_data)  

# Add the reason count if available
motif_counts <- rowSums(motif_data) # Count the occurrence of motifs (adjust as necessary)

# Check the dimensions of the motif_data object
dim(motif_data) # Number of rows and columns
## [1] 120 633
# Check the length of tf_names and motif_counts
tf_names_length <- length(tf_names)
motif_counts_length <- length(motif_counts)

# Print the lengths for diagnosis
cat("Length of tf_names:", tf_names_length, "\n")
## Length of tf_names: 633
cat("Length of motif_counts:", motif_counts_length, "\n")
## Length of motif_counts: 120
# Verify that the dimensions of motif_data correspond to the number of TFs and motifs
motif_data_dims <- dim(motif_data)
cat("Dimensions of motif_data (rows, columns):", motif_data_dims, "\n")
## Dimensions of motif_data (rows, columns): 120 633
# Check whether the number of reasons is greater or lesser
if (tf_names_length > motif_counts_length) {
  # Check additional columns
  tf_names <- tf_names[1:motif_counts_length] # Adjust to the length of motif_counts
} else {
  # Adjust motif_counts to match tf_names
  motif_counts <- motif_counts[1:tf_names_length]
}

# Now, I have created the data frame with adjusted lengths
motif_summary <- data.frame(
  tf_name = tf_names,
  motif_count = motif_counts
)

# Check the correspondence between TF names and the columns in motif_data
all(tf_names %in% colnames(motif_data)) # Should return TRUE if all TF names are present
## [1] TRUE
# Sort and identify key TFs
tf_summary <- motif_summary[order(motif_summary$motif_count, decreasing = TRUE), ]
top_tf_summary <- head(tf_summary, 130) # Adjust the number as required.

# Mapping Entrez IDs to gene symbols
gene_symbols <- mapIds(org.Hs.eg.db, keys = rownames(top_tf_summary), column = "SYMBOL", keytype = "ENTREZID", multiVals = "first")
## 'select()' returned 1:1 mapping between keys and columns
# Replace rownames with gene symbols
rownames(top_tf_summary) <- gene_symbols

top_tf_summary$motif_id <- rownames(top_tf_summary)

# Combine with the table of TF names
motif1 <- merge(top_tf_summary, motif_info, by.x = "tf_name", by.y = "motif_id")

# Reorganise columns for better viewing
motif2<- motif1[, c("motif_id", "tf_name.y", "motif_count")]
colnames(motif2) <- c("motif_id", "tf_name.y", "motif_count")

# View
print(motif2)
##     motif_id           tf_name.y motif_count
## 1       OLR1                 EN1         140
## 2     ZNF316               FOXF2         162
## 3      NAMPT               FOXD1         118
## 4      PPARG               FOXL1         157
## 5       SMOX               FOXI1         130
## 6      PTGS2               HNF1A         130
## 7    ZC3H12A               NHLH1         110
## 8     CLEC4D                IRF1         101
## 9      SPON2                IRF2         126
## 10    CXCL13         MZF1(var.2)          97
## 11      GJB6            MAX::MYC         176
## 12    FAXDC2               PPARG         149
## 13     RSAD2                PAX4         140
## 14  PPARGC1A                PAX6         131
## 15    AKAP13                PBX1         134
## 16     IL17F                RORA         152
## 17      GBP5         RORA(var.2)         134
## 18     MUCL1               RREB1         149
## 19   NOXRED1           RXRA::VDR         120
## 20      GZMB                ELK4         128
## 21      CCR7                SOX9         198
## 22      CD38                 SRF         122
## 23     ACKR2                 SRY         121
## 24   EFCAB13          TAL1::TCF3         159
## 25      IL1B                 YY1         120
## 26     CTLA4                 REL         136
## 27    CYP1A1                RELA         131
## 28    ZNF483         NR1H2::RXRA         115
## 29     KANK4          NFIC::TLX1         118
## 30      TYMP             ZNF354C         124
## 31   ADAMTS9               HINFP         159
## 32      NOS2                ELF5         134
## 33     IFIT3               STAT1         115
## 34  SERPINB1                REST         144
## 35       EGF                CTCF         126
## 36      IGF2         GATA1::TAL1         114
## 37      IFNG               STAT3         114
## 38      EGFR          EWSR1-FLI1          90
## 39       ALB              NFATC2         131
## 40      IL21               HNF1B         137
## 41    FCGR1A               INSM1         116
## 42     SAMD9               FOXO3         161
## 43    FCGR3A          RARA::RXRA         160
## 44      DKK1               NR4A2         167
## 45      CRB1               PLAG1         136
## 46      NRG1                ESR2         108
## 47       FOS         ARNT::HIF1A         138
## 48     HYAL4                DUX4         136
## 49       PI3                FLI1         174
## 50   SLC7A11                 FOS         144
## 51      FRZB               FOSL2         122
## 52      FUT2               FOXH1         169
## 53      RORC                HSF1         154
## 54      IFI6                 JUN         168
## 55     GATA3          JUN(var.2)         127
## 56      GBP1         JUND(var.2)         123
## 57    IL36RN               MEF2C         135
## 58      GJB2           MAF::NFE2         139
## 59      IL37               NR2C2         146
## 60   PLA2G4D                NRF1         153
## 61       GPT              POU2F2         119
## 62     CD274 SMAD2::SMAD3::SMAD4         129
## 63     CXCL2        STAT1::STAT2         175
## 64      ICOS              TCF7L2         119
## 65      GZMA              ZBTB33         167
## 66     IL2RA               FOXP2         134
## 67       IL5              SREBF1         167
## 68       IL6              SREBF2         148
## 69     CXCL8               THAP1         206
## 70     CXCR2                KLF5         123
## 71     IL12B               DMRT3         154
## 72      IL13               FOXG1         156
## 73   TNFRSF9                LBX1         167
## 74     IL17A              NFATC3         133
## 75    CXCL10              POU6F1         115
## 76      IRS1                SHOX         143
## 77    ITGA2B                ALX3         120
## 78      ACP7              BARHL2         121
## 79      MEFV             BHLHE41         160
## 80      MMP1               CENPB         129
## 81      MMP9               CREB3         193
## 82       MX1                 DBP         113
## 83      NKG7                ELF4         123
## 84      IL22                 EN2         128
## 85    NT5C3A                ESX1         137
## 86      PER1                ETV6         137
## 87     HERC6                GCM1         120
## 88      PRF1               GRHL1         163
## 89    ZNF415                 GSC         126
## 90      RETN                HEY2         113
## 91     CCND1              HOXC11         184
## 92    S100A8                IRF8         141
## 93    S100A9                IRF9         107
## 94   S100A12                 ISX         116
## 95     S100P                JDP2         106
## 96     BGLAP         JDP2(var.2)         138
## 97     CCL20               KLF13         234
## 98     PRDM1                LHX6         155
## 99      SELL               MEF2B         124
## 100     NOD2               MEOX1         137
## 101    CSMD1               MIXL1         111
## 102   SLC1A2                 MLX         103
## 103     SOX4              MLXIPL         129
## 104    STAT1                 MSC         108
## 105     SYT1                MSX1         141
## 106   TGFBR3                MYF6         163
## 107    TRAF5             NEUROD2         102
## 108 INS-IGF2             NEUROG2          87
## 109    RGPD6                NFIA         144
## 110    CALD1                NFIX         117
## 111    FOSL1              NKX2-3         117
## 112    CAPS2              NKX2-8         128
## 113    APOL1              NKX6-1         129
## 114     JRKL              NKX6-2         135
## 115    HCAR3               OLIG2         125
## 116     CD8A                PAX7         104
## 117   ADIPOQ              POU4F2          99
## 118     CD80                 SP4          85
## 119     AIM2               SPDEF         100
## 120     CD36                SPIC         188